Programmable nuclease compositions and methods of use thereof

ABSTRACT

Described herein are devices, systems, fluidic devices, kits, and methods for detection of target nucleic acids associated with diseases, cancers, genetic disorders, a genotype, a phenotype, or ancestral origin. The devices, systems, fluidic devices, kits, and methods may comprise reagents of a guide nucleic acid targeting a target nucleic acid, a programmable nuclease, and a single stranded detector nucleic acid with a detection moiety. The target nucleic acid of interest may be indicative of a disease, and the disease may be communicable diseases, or of a cancer or genetic disorder. The target nucleic acid of interest may be indicative of a genotype, a phenotype, or ancestral origin.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of PCT International Application No.PCT/US2019/044763, which claims priority to and benefit from U.S.Provisional Application Nos. 62/713,379 filed Aug. 1, 2018; 62/722,024,filed Aug. 23, 2018; 62/787,123 filed Dec. 31, 2018; 62/788,701 filedJan. 4, 2019; 62/788,702 filed Jan. 4, 2019; 62/863,184 filed Jun. 18,2019; and 62/879,332, filed Jul. 26, 2019, the entire contents of eachof which are herein incorporated by reference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Sep. 13, 2019, isnamed 53694-705_304_SL.txt and is 757,085 bytes in size.

BACKGROUND

Ailments, such as cancer, genetic disorders, or communicable diseases,can be difficult to detect. Various communicable diseases can easilyspread from an individual or environment to an individual. Thesediseases may include but are not limited to human immunodeficiency virus(HIV), human papillomavirus (HPV), chlamydia, gonorrhea, syphilis,trichomoniasis, sexually transmitted infection, malaria, Dengue fever,Ebola, chikungunya, and leishmaniasis. Individuals with one or more ofthese ailments may have poor outcomes, including severe symptoms thatcan lead to death. The detection of the ailments, especially at theearly stages of disease or infection, may provide guidance on treatmentor intervention to reduce the progression or transmission of theailment.

SUMMARY

In various aspects, the present disclosure provides a device formeasuring a signal comprising: i) a first chamber comprising a sampleand a buffer for lysing the sample; ii) a second chamber, fluidicallyconnected by a first pneumatic valve to the first chamber, wherein thesecond chamber comprises a programmable nuclease and a reportercomprising a nucleic acid and a detection moiety, and wherein the secondchamber is coupled to a measurement device for measuring the signal fromthe detection moiety produced by cleavage of the nucleic acid of thereporter.

In some aspects, the device further comprises: iii) a third chamberfluidically connected by the first pneumatic valve to the first chamberand connected by a second pneumatic valve to the second chamber. In someaspects, the first pneumatic valve fluidically connecting the firstchamber and the second chamber comprises a first channel adjacent to afirst microfluidic channel connecting the first chamber and the secondchamber. In some aspects, the first pneumatic valve fluidicallyconnecting the first chamber and the third chamber comprises a secondchannel adjacent to a second microfluidic channel connecting the firstchamber and the third chamber. In some aspects, the second pneumaticvalve fluidically connecting the second chamber and the third chambercomprises a third channel adjacent to a third microfluidic channelconnecting the second chamber and the third chamber.

In some aspects, the first channel, the second channel, or the thirdchannels are connected to an air manifold. In some aspects, more thanone chamber comprising a programmable nuclease and a reporter arefluidically connected to a single chamber comprising the sample. In someaspects, more than one chamber comprising a programmable nuclease and areporter are fluidically connected to a single chamber comprising aforward primer, a reverse primer, a dNTP, and a polymerase.

In various aspects, the present disclosure provides a device formeasuring a signal comprising: a sliding layer comprising a channel withan opening at a first end of the channel and an opening at a second endof the channel; and a fixed layer comprising: i) a first chamber havingan opening; ii) a second chamber having an opening, wherein the secondchamber comprises a programmable nuclease and a reporter comprising anucleic acid and a detection moiety; iii) a first side channel having anopening aligned with the opening of the first chamber; and iv) a secondside channel having an opening aligned with the opening of the secondchamber, wherein the sliding layer and the fixed layer move relative toeach other to fluidically connect the first chamber and the first sidechannel via the opening at the first end of the channel, the opening atthe second end of the channel, the opening of the first chamber, and theopening of the first side channel, and wherein the sliding layer and thefixed layer move relative to each other to fluidically connect thesecond chamber and the second side channel via the opening at the firstend of the channel, the opening at the second end of the channel, theopening of the second chamber, and the opening of the second sidechannel.

In some aspects, the fixed layer further comprises i) a third chamberhaving an opening; and ii) a third side channel having an openingaligned with the opening of the third chamber, wherein the sliding layerand the fixed layer move relative to each other to fluidically connectthe third chamber and the third side channel via the opening at thefirst end of the channel, the opening at the second end of the channel,the opening of the third chamber, and the opening of the third sidechannel. In some aspects, the second chamber is coupled to a measurementdevice for measuring the signal from the detection moiety produced bycleavage of the nucleic acid of the reporter. In some aspects, theopening of the first end of the channel overlaps with the opening of thefirst chamber and the opening of the second end of the channel overlapswith the opening of the first side channel.

In some aspects, the opening of the first end of the channel overlapswith the opening of the second chamber and the opening of the second endof the channel overlaps with the opening of the second side channel. Insome aspects, the opening of the first end of the channel overlaps withthe opening of the third chamber and the opening of the second end ofthe channel overlaps with the opening of the third channel. In someaspects, the first side channel, the second side channel, and the thirdside channel are fluidically connected to a mixing chamber.

In some aspects, the third chamber comprises a forward primer, a reverseprimer, a dNTP, an NTP, a polymerase, a reverse transcriptase, a T7polymerase, or any combination thereof. In some aspects, the forwardprimer, the reverse primer, or both comprises a T7 promoter. In someaspects, the second chamber comprises a guide nucleic acid. In someaspects, the programmable nuclease, the reporter, the guide nucleicacid, the forward primer, the reverse primer, the dNTP, the NTP, thepolymerase, the reverse transcriptase, the T7 promoter, the T7polymerase, or any combination thereof is lyophilized or vitrified.

In some aspects, the second chamber is optically connected to aspectrophotometric measurement device or a fluorescence measurementdevice. In some aspects, the second chamber comprises a metal leadadapted for measurement of a change in current. In some aspects, thefirst chamber holds a volume of about 200 μL, the second chamber holds avolume of about 20 μL, and the third chamber holds a volume of about 20μL. In some aspects, the second chamber comprises a plurality of guideRNAs.

In some aspects, the device comprises from 2 to 20 chambers comprising aprogrammable nuclease, a guide nucleic acid, and a reporter, wherein adetection chamber of the from 2 to 20 chambers comprises a unique guidenucleic acid. In some aspects, the reporter is a hybrid reporter havingat least one ribonucleotide and at least one deoxyribonucleotide. Insome aspects, the reporter is immobilized to a surface. In some aspects,the surface is a surface of the first chamber or a surface of a bead.

In various aspects, the present disclosure provides a device comprising:a chamber comprising i) a programmable nuclease; and ii) an immobilizedreporter comprising a nucleic acid, an affinity molecule, and adetection moiety; and a lateral flow strip comprising: i) a first regioncomprising a capture molecule specific for the affinity molecule; andii) a second region comprising an antibody, wherein the first region isupstream of the second region and the chamber is upstream of the lateralflow strip and wherein the first molecule binds to the second molecule.

In some aspects, the first molecule is conjugated to a 3′ end or a 5′end of the nucleic acid, and wherein the first molecule is directlyconjugated to the detection moiety. In some aspects, the detectionmoiety comprises a fluorophore. In some aspects, the antibody on thesecond region is specific for an antibody-coated nanoparticle. In someaspects, the antibody-coated nanoparticle binds the fluorophore. In someaspects, the chamber further comprises a second immobilized reportercomprising a second nucleic acid, a second detection moiety, and thefirst molecule.

In some aspects, the first molecule is conjugated to a 3′ end or a 5′end of the second nucleic acid, and wherein the first molecule isdirectly conjugated to the second detection moiety. In some aspects, thelateral flow strip comprises a third region comprising a secondantibody. In some aspects, the antibody binds the fluorophore and thesecond antibody binds the second fluorophore. In some aspects, theimmobilized reporter, the second immobilized reporter, or both areconjugated to a magnetic bead.

In some aspects, the chamber interfaces with a magnet. In some aspects,the device is connected to a sample prep device comprising a samplechamber, upstream, of an amplification chamber, upstream of the chamber.In some aspects, the sample chamber, the amplification chamber, thereaction chamber, and the lateral flow strip are separated by asubstrate. In some aspects, each chamber of the sample prep devicecomprises a notch preventing fluid flow. In some aspects, the sampleprep device comprises a rotatable element and wherein the rotatableelement controls fluid flow between chambers.

In various aspects, the present disclosure provides a method ofdetecting a presence or an absence of a target nucleic acid in a sample,the method comprising: contacting a first volume to a second volume,wherein the first volume comprises the sample and the second volumecomprises: i) a guide nucleic acid having at least 10 nucleotidesreverse complementary to a target nucleic acid in the sample; and ii) aprogrammable nuclease activated upon binding of the guide nucleic acidto the target nucleic acid; iii) a reporter comprising a nucleic acidand a detection moiety, wherein the second volume is at least 4-foldgreater than the first volume; and detecting the presence or the absenceof the target nucleic acid by measuring a signal produced by cleavage ofthe nucleic acid of the reporter, wherein cleavage occurs when theprogrammable nuclease is activated.

In various aspects, the present disclosure provides any of the abovedevices for use in a method of detecting a presence of an absence of atarget nucleic acid in a sample, the method comprising: contacting afirst volume to a second volume, wherein the first volume comprises thesample and the second volume comprises: i) a guide nucleic acid havingat least 10 nucleotides reverse complementary to a target nucleic acidin the sample; and ii) a programmable nuclease activated upon binding ofthe guide nucleic acid to the target nucleic acid; iii) a reportercomprising a nucleic acid and a detection moiety, wherein the secondvolume is at least 4-fold greater than the first volume; and detectingthe presence or the absence of the target nucleic acid by measuring asignal produced by cleavage of the nucleic acid of the reporter, whereincleavage occurs when the programmable nuclease is activated.

In various aspects, the present disclosure provides a method comprisingof detecting a presence of an absence of a first target nucleic acid, asecond target nucleic acid, or both in a sample, the method comprising:contacting the sample to i) a first guide nucleic acid having at least10 nucleotides reverse complementary to the first target nucleic acidfrom an organism and a first programmable nuclease activated uponbinding of the first guide nucleic acid to the first target nucleicacid; and ii) a second guide nucleic acid having at least 10 nucleotidesreverse complementary to the second target nucleic acid from a drugresistant allele of the organism and a second programmable nucleaseactivated upon binding of the second guide nucleic acid to the secondtarget nucleic acid, wherein the first programmable nuclease and thesecond programmable nuclease are different; detecting a presence or anabsence of the first target nucleic acid by measuring a first signalproduced by cleavage of a nucleic acid of a first reporter, whereincleavage occurs when the first programmable nuclease is activated; anddetecting a presence or an absence of the second target nucleic acid bymeasuring a second signal produced by cleavage of a nucleic acid of thesecond reporter, wherein cleavage occurs when the second programmablenuclease is activated.

In various aspects, the present disclosure provides any of the abovedevices for use in a method of detecting a presence of an absence of afirst target nucleic acid, a second target nucleic acid, or both in asample, the method comprising: contacting the sample to i) a first guidenucleic acid having at least 10 nucleotides reverse complementary to thefirst target nucleic acid from an organism and a first programmablenuclease activated upon binding of the first guide nucleic acid to thefirst target nucleic acid; and ii) a second guide nucleic acid having atleast 10 nucleotides reverse complementary to the second target nucleicacid from a drug resistant allele of the organism and a secondprogrammable nuclease activated upon binding of the second guide nucleicacid to the second target nucleic acid, wherein the first programmablenuclease and the second programmable nuclease are different; detecting apresence or an absence of the first target nucleic acid by measuring afirst signal produced by cleavage of a nucleic acid of a first reporter,wherein cleavage occurs when the first programmable nuclease isactivated; and detecting a presence or an absence of the second targetnucleic acid by measuring a second signal produced by cleavage of anucleic acid of the second reporter, wherein cleavage occurs when thesecond programmable nuclease is activated.

In some aspects, the first target nucleic acid and the second targetnucleic acid are different. In some aspects, the nucleic acid of thefirst reporter is a DNA nucleic acid and wherein the nucleic acid of thesecond reporter is an RNA nucleic acid.

In various aspects, the present disclosure provides a method ofdetecting a target nucleic acid in a sample, the method comprising:contacting the sample to: i) a guide nucleic acid having at least 10nucleotides reverse complementary to the target nucleic acid; and ii) aprogrammable nuclease activated upon binding of the guide nucleic acidto the target nucleic acid; iii) a hybrid reporter comprising adetection moiety and a nucleic acid having at least one ribonucleotideand at least one deoxyribonucleotide; detecting a presence or an absenceof the target nucleic acid by measuring a signal produced by cleavage ofthe nucleic acid of the hybrid reporter, wherein cleavage occurs whenthe programmable nuclease is activated.

In various aspects, the present disclosure provides any of the abovedevices for use in a method of detecting a target nucleic acid in asample, the method comprising: contacting the sample to: i) a guidenucleic acid having at least 10 nucleotides reverse complementary to thetarget nucleic acid; and ii) a programmable nuclease activated uponbinding of the guide nucleic acid to the target nucleic acid; iii) ahybrid reporter comprising a detection moiety and a nucleic acid havingat least one ribonucleotide and at least one deoxyribonucleotide;detecting a presence or an absence of the target nucleic acid bymeasuring a signal produced by cleavage of the nucleic acid of thehybrid reporter, wherein cleavage occurs when the programmable nucleaseis activated.

In various aspects, the present disclosure provides a method foridentifying a treatment for a subject comprising: measuring a signal by:contacting a sample comprising a target nucleic acid from the subjectto: i) a guide nucleic acid having at least 10 nucleotides reversecomplementary to the target nucleic acid; and ii) a programmablenuclease activated upon binding of the guide nucleic acid to the targetnucleic acid; iii) a reporter comprising a nucleic acid and a detectionmoiety; and measuring the signal produced by cleavage of the nucleicacid of the reporter, wherein cleavage occurs when the programmablenuclease is activated; and identifying the treatment to administer tothe subject.

In various aspects, the present disclosure provides any of the abovedevices for use in a method for identifying a treatment for a subjectcomprising: measuring a signal by: contacting a sample comprising atarget nucleic acid from the subject to: i) a guide nucleic acid havingat least 10 nucleotides reverse complementary to the target nucleicacid; and ii) a programmable nuclease activated upon binding of theguide nucleic acid to the target nucleic acid; iii) a reportercomprising a nucleic acid and a detection moiety; and measuring thesignal produced by cleavage of the nucleic acid of the reporter, whereincleavage occurs when the programmable nuclease is activated; andidentifying the treatment to administer to the subject.

In some aspects, the sample is in a first volume and wherein the guidenucleic acid, the programmable nuclease, and the reporter are in asecond volume. In some aspects, the second volume is at least 4-foldgreater than the first volume. In some aspects, the second volume is atleast 10-fold greater than the first volume. In some aspects, thereporter is a hybrid reporter having at least one ribonucleotide and atleast one deoxyribonucleotide.

In some aspects, the method comprises amplifying the target nucleicacid, reverse transcribing the target nucleic acid, in vitrotranscription of the target nucleic acid, or any combination thereof. Insome aspects, the amplifying comprises using a phosphorothioated forwardprimer, a phosphorothioated reverse primer, or both. In some aspects,the amplifying comprises isothermal amplification. In some aspects, theamplifying comprises thermal amplification.

In some aspects, the amplifying comprises recombinase polymeraseamplification (RPA), transcription mediated amplification (TMA), stranddisplacement amplification (SDA), helicase dependent amplification(HDA), loop mediated amplification (LAMP), rolling circle amplification(RCA), single primer isothermal amplification (SPIA), ligase chainreaction (LCR), simple method amplifying RNA targets (SMART), orimproved multiple displacement amplification (IMDA), or nucleic acidsequence-based amplification (NASBA). In some aspects, the amplifyingcomprises recombinase polymerase amplification (RPA). In some aspects,the amplifying comprises loop mediated amplification (LAMP).

In some aspects, the amplifying the target nucleic acid, the reversetranscribing the target nucleic acid, the in vitro transcription of thetarget nucleic acid, or any combination thereof is in the same reactionas the detecting and the measuring. In some aspects, the method furthercomprises removing non-target nucleic acids with an exonuclease. In someaspects, the nucleic acid of the reporter is conjugated at its 3′ end or5′ end to an affinity molecule, wherein the affinity molecule isdirectly conjugated to the detection moiety.

In some aspects, the guide nucleic acid, the programmable nuclease, andthe reporter are present in a single chamber. In some aspects, thesingle chamber is fluidically connected to a second chamber via a firstpneumatic valve, wherein the second chamber comprises the sample. Insome aspects, a third chamber is positioned between the second chamberand the single chamber, wherein the third chamber comprises a dNTP, aforward primer, a reverse primer, and a polymerase. In some aspects, thethird chamber is fluidically connected to the single chamber via asecond pneumatic valve and wherein the third chamber is fluidicallyconnected to the second chamber via a third pneumatic valve.

In some aspects, the method further comprises: opening the thirdpneumatic valve and moving 1 to 10 μL of the sample from the secondchamber to the third chamber; and opening the second pneumatic valve andmoving 1 to 10 μL of the sample from the third chamber to the singlechamber, or opening the first pneumatic valve and moving 1 to 10 μL ofthe sample from the second chamber to the single chamber. In someaspects, the method further comprises incubating the sample in thesingle chamber for from 1 minute to 10 minutes. In some aspects, thesingle chamber has an opening.

In some aspects, the single chamber and a second chamber having anopening are positioned in a fixed layer, wherein the second chambercomprises the sample, and wherein the fixed layer is coupled to asliding layer comprising a channel having a first opening and a secondopening. In some aspects, the fixed layer further comprises a thirdchamber having an opening, wherein the third chamber comprises a dNTP, aforward primer, a reverse primer, and a polymerase. In some aspects, theopening in the second chamber is aligned with an opening in a first sidechannel, the opening in the third chamber is aligned with an opening ina second side channel, and the opening in the single chamber is alignedwith an opening in a third side channel.

In some aspects, the method comprises one or more of the followingsteps: sliding the sliding layer to overlap the opening of the secondchamber with the opening of the channel; moving the sample from thesecond chamber into the channel; aspirating the sample from the channelinto the first side channel and mixing; sliding the sliding layer tooverlap the opening of the channel with the opening of the thirdchamber; dispensing the sample into the third chamber; moving the samplefrom the third chamber into the channel; aspirating the sample from thechannel into the second side channel and mixing; sliding the slidinglayer to overlap the opening of the channel with the opening of thesingle chamber; and dispensing the sample into the single chamber.

In some aspects, the method comprises one or more of the followingsteps: sliding the sliding layer to overlap the opening of the secondchamber with the opening of the channel; moving the sample from thesecond chamber into the channel; aspirating the sample from the channelinto the first side channel and mixing; sliding the sliding layer tooverlap the opening of the channel with the opening of the singlechamber; and dispensing the sample into the single chamber. In someaspects, the measuring comprises fluorescence imaging,spectrophotometry, or electrochemical measurements.

In some aspects, the programmable nuclease, the reporter, the guidenucleic acid, or any combination thereof are lyophilized or vitrified.In some aspects, the guide nucleic acid comprises from 2 to 20 guideRNAs and wherein a guide RNA of the from 2 to 20 guide RNAs is a uniqueguide RNA.

In some aspects, the reporter is immobilized to a surface in the singlechamber. In some aspects, the surface is a surface of the single chamberor a surface of a bead. In some aspects, the target nucleic acid is frominfluenza A virus, influenza B virus, RSV, dengue virus, West Nilevirus, Hepatitis Virus C, Hepatitis Virus A, Hepatitis Virus B,papillomavirus, HIV, chlamydia, gonorrhea, syphilis, trichomoniasis,borrelia, zika virus, or a sepsis causing organism.

In some aspects, the programmable nuclease is a programmable Type VCRISPR/Cas enzyme. In some aspects, the programmable Type V CRISPR/Casenzyme is a programmable Cas12 nuclease. In some aspects, theprogrammable Cas12 nuclease is Cas12a, Cas12b, Cas12c, Cas12d, orCas12e.

In some aspects, the programmable Type V CRISPR/Cas enzyme is aprogrammable Cas14 nuclease. In some aspects, the programmable Cas14nuclease is Cas14a, Cas14b, Cas14c, Cas14d, Cas14e, Cas14f, Cas14g, orCas14h. In some aspects, the programmable nuclease is a programmableType VI CRISPR/Cas enzyme. In some aspects, the programmable Type VICRISPR/Cas enzyme is a programmable Cas13 nuclease. In some aspects, theprogrammable Cas13 nuclease is Cas13a, Cas13b, Cas13c, Cas13d, orCas13e.

In various aspects, the present disclosure provides the use of aprogrammable nuclease in a device for measuring a signal, wherein thedevice comprises: i) a first chamber comprising a sample and a bufferfor lysing the sample; ii) a second chamber, fluidically connected by afirst pneumatic valve to the first chamber, wherein the second chambercomprises the programmable nuclease and a reporter comprising a nucleicacid and a detection moiety, and wherein the second chamber is coupledto a measurement device for measuring the signal from the detectionmoiety produced by cleavage of the nucleic acid of the reporter.

In various aspects, the present disclosure provides the use of aprogrammable nuclease in a device for measuring a signal, wherein thedevice comprises: a sliding layer comprising a channel with an openingat a first end of the channel and an opening at a second end of thechannel; and a fixed layer comprising: iii) a first chamber having anopening; iv) a second chamber having an opening, wherein the secondchamber comprises the programmable nuclease and a reporter comprising anucleic acid and a detection moiety; v) a first side channel having anopening aligned with the opening of the first chamber; and vi) a secondside channel having an opening aligned with the opening of the secondchamber, wherein the sliding layer and the fixed layer move relative toeach other to fluidically connect the first chamber and the first sidechannel via the opening at the first end of the channel, the opening atthe second end of the channel, the opening of the first chamber, and theopening of the first side channel, and wherein the sliding layer and thefixed layer move relative to each other to fluidically connect thesecond chamber and the second side channel via the opening at the firstend of the channel, the opening at the second end of the channel, theopening of the second chamber, and the opening of the second sidechannel.

In various aspects, the present disclosure provides the use of aprogrammable nuclease in a device for measuring a signal, wherein thedevice comprises: a chamber comprising i) a programmable nuclease; andii) an immobilized reporter comprising a nucleic acid, an affinitymolecule, and a detection moiety; and a lateral flow strip comprising:i) a first region comprising a capture molecule specific for theaffinity molecule; and ii) a second region comprising an antibody,wherein the first region is upstream of the second region and thechamber is upstream of the lateral flow strip and wherein the firstmolecule binds to the second molecule.

In various aspects, the present disclosure provides the use of a hybridreporter in a method of detecting a target nucleic acid in a sample, themethod comprising: contacting the sample to: i) a guide nucleic acidhaving at least 10 nucleotides reverse complementary to the targetnucleic acid; and ii) a programmable nuclease activated upon binding ofthe guide nucleic acid to the target nucleic acid; iii) a hybridreporter comprising a detection moiety and a nucleic acid having atleast one ribonucleotide and at least one deoxyribonucleotide; detectinga presence or an absence of the target nucleic acid by measuring asignal produced by cleavage of the nucleic acid of the hybrid reporter,wherein cleavage occurs when the programmable nuclease is activated.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in thisspecification are herein incorporated by reference to the same extent asif each individual publication, patent, or patent application wasspecifically and individually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the disclosure are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present disclosure will be obtained by reference tothe following detailed description that sets forth illustrativeembodiments, in which the principles of the disclosure are utilized, andthe accompanying drawings of which:

FIG. 1 shows the fluorescent signal of exemplary RNA reporter moleculesfor use with LbuCas13a. The bars from left to right for each reporterwere performed with no enzyme (no LbuCas13a); with RNase A; withLbuCas13a but without a target nucleic acid; or with LbuCas13a and withthe target nucleic acid. FAM-UU: /56-FAM/TTrUrUTT(SEQ ID NO: 5)/3IABkFQ/; FAM-UU-long: 56-FAM/TTTTrUrUTTTT(SEQ ID NO: 4)/3 IABkFQ/;FAM-AU: /56-FAM/TArArUGC(SEQ ID NO: 6)/3 IABkFQ/; FAM-UG:/56-FAM/TArUrGGC(SEQ ID NO: 7)/3 IABkFQ/; FAM-U10:/56-FAM/rUrUrUrUrUrUrUrUrUrU(SEQ ID NO: 3)/3 IABkFQ/; FAM-U5:/56-FAM/rUrUrUrUrU(SEQ ID NO: 1)/3 IABkFQ/; FAM-U8:/56-FAM/rUrUrUrUrUrUrUrU(SEQ ID NO: 2)/3IABkFQ/; RNAse Alert:Proprietary reporter from Integrated DNA Technologies RNaseAlertSubstrate Nuclease Detection System. rU=uracil ribonucleotide;rA=adenine ribonucleotide; rG=guanine ribonucleotide. 56-FAM: 5′6-Fluorescein dye; 3IABkFQ: 3′ Iowa Black FQ.

FIG. 2 shows the fluorescent signal of samples with various combinationsof no RNA, RNA from E. coli only (comprises target RNA from E. coli),RNA from Chlamydia only (comprises target RNA from Chlamydia), or RNAfrom both Chlamydia and E. coli (comprises target RNA from E. coli andChlamydia) mixed with CRISPR RNAs (crRNAs) for the Chlamydia RNA, crRNAsfor the E. coli RNA, or crRNAs for Chlamydia RNA mixed with crRNAs forE. coli RNA.

FIG. 3 shows the fluorescent signal for three different crRNAs eitherindividually or as a mixture of all three crRNAs, with either no targetRNA or a target RNA with sites for all three crRNAs.

FIG. 4 shows the autofluorescent signal of urine at differentwavelengths associated with detection of different fluorophores.

FIG. 5A shows the fluorescent signal of urine with Cas13a and targetRNAs with no RNAse inhibitor (left panel), RiboLock RNAse inhibitor(middle panel), and polyvinyl sulfonic acid (PVS) (right panel). Each ofthese conditions were tested in a urine fraction of 0 (buffer only) or aurine fraction of 0.18 (18% urine in buffer) and either without or withtarget RNA. * Indicate data was cut-off.

FIG. 5B shows a rescaled y-axis for the left panel of FIG. 5A.

FIG. 6 shows the normalized fluorescence signal of FAM, AlexaFluor594,ATTO633 (red-emitting fluorescence label), TYE665, and IRDYE700fluorophores in human urine, which was normalized against the ratio offluorescence between urine with or without RNase inhibitor for the FAMfluorophore.

FIG. 7A shows the background subtracted fluorescent signal of RNAreporter molecules with Cas13a and 100 fM of target RNA in either theoriginal Cas13a buffer or an enhanced buffer (MBuffer1). FAM-U5:/56-FAM/rUrUrUrUrU(SEQ ID NO: 1)/3IABkFQ/; TYE665-U5:/5TYE665/rUrUrUrUrU(SEQ ID NO: 1)/3IAbRQSp/; IRDYE700-U5:/5IRD700/rUrUrUrUrU(SEQ ID NO: 1)/3IRQC1N/. rU=uracil ribonucleotide.56-FAM: 5′ 6-Fluorescein dye; 3IABkFQ: 3′ Iowa Black FQ; 5TYE665: 5′ TYE665; 3IAbRQsp: 3′Iowa Black RQ; 5IRD700: 5′ IRDye 700; 3IRQC1N: IRDyeQC-1 quencher.

FIG. 7B shows the background subtracted fluorescent signal of RNAreporter molecules with Cas13a and 10 pM of target RNA in either theoriginal Cas13a buffer or an enhanced buffer (MBuffer1) in urine.FAM-U5: /56-FAM/rUrUrUrUrU(SEQ ID NO: 1)/3IABkFQ/; TYE665-U5:/5TYE665/rUrUrUrUrU(SEQ ID NO: 1)/3IAbRQSp/; IRDYE700-U5:/5IRD700/rUrUrUrUrU(SEQ ID NO: 1)/3IRQC1N/. rU=uracil ribonucleotide.56-FAM: 5′ 6-Fluorescein dye; 3IABkFQ: 3′ Iowa Black FQ; 5TYE665: 5′TYE665; 3IAbRQsp: 3′ Iowa Black RQ; 5IRD700: 5′ IRDye 700; 3IRQC1N: QC-1quencher.

FIG. 8A is a schematic showing a guide nucleic acid (gRNA) for detectionof a species-specific locus of P. falciparum, a gRNA for detection of aWT allele of kelch13, and a gRNA for detection of a C580Y allele ofkelch13. The gRNA for detection of a WT allele of kelch13 binds to theWT allele of kelch13, but does not bind to the kelch13 C580Y allele. ThegRNA for detection of the kelch13 C580Y allele binds to the kelch13C580Y allele, but does not bind to the kelch13 WT allele.

FIG. 8B shows Cas12a is capable of discriminating between WT and a SNPresponsible for Artemisinin resistance in P. falciparum. For the WT, thegRNA that binds to the WT nucleic acid molecule (WT gRNA) producesfluorescence in the presence of the WT target nucleic acid molecule (WTtarget) but not in the presence of the target nucleic acid moleculecomprising the SNP (mut target). For the SNP, the gRNA that binds to thetarget nucleic acid molecule comprising the SNP (mut gRNA) producesfluorescence in the presence of the target nucleic acid moleculecomprising the SNP (mut target), but not in the presence of the WTtarget.

FIG. 8C shows species-specific detection of 16S of N. gonorrhea by Cas13using a reporter molecule (/5-6FAM/rUrUrUrUrU(SEQ ID NO: 1)/3IABkFQ/)and detection of an azithromycin resistance SNP for N. gonorrhea (23Smutant) versus wild-type (23S WT) N. gonorrhea by Cas12 using a reportermolecule (/AF594/TTATTATT/3IAbRQSp/), all in a single reaction. The topgrid shows detection of N. gonorrhea using a Cas13 species-specific 16SgRNA and detection of WT 23S using a Cas12 gRNA targeting the 23S WT,indicating the N. gonorrhea is susceptible to antibiotic treatment usingazithromycin. The bottom grid shows detection of N. gonorrhea using aCas13 species-specific 16S gRNA and detection of mutant 23S using aCas12 gRNA targeting the 23S mutant, indicating the N. gonorrhea isresistant to antibiotic treatment using azithromycin.

FIG. 9 shows a schematic illustrating a workflow of a CRISPR-Casreaction. Step 1 shown in the workflow is sample preparation. Step 2shown in the workflow is nucleic acid amplification. Step 3 shown in theworkflow is Cas reaction incubation. Step 4 shown in the workflow isdetection (readout). Non-essential steps are shown as oval circles.Steps 1 and 2 are not essential, and steps 3 and 4 can occurconcurrently, if detection and readout are incorporated to the CRISPRreaction.

FIG. 10 shows an example fluidic device for sample preparation that maybe used in Step 1 of the workflow schematic of FIG. 9 . The samplepreparation fluidic device shown in this figure can process differenttypes of biological sample: finger-prick blood, urine, or swabs withfecal, cheek, or other collection.

FIG. 11 shows three example fluidic devices for a Cas reaction with afluorescence or electrochemical readout that may be used in Step 2 toStep 4 of the workflow schematic of FIG. 9 . This figure shows that thedevice performs three iterations of Steps 2 through 4 of the workflowschematic of FIG. 9 . An exploded view diagram summarizing thefluorescence and electrochemical processes that may be used fordetection of the reaction are shown in FIG. 12 .

FIG. 12 shows schematic diagrams of a readout process that may be usedincluding (a) fluorescence readout and (b) electrochemical readout.

FIG. 13 shows an example fluidic device for coupled invertase/Casreactions with colorimetric or electrochemical/glucometer readout. Thisdiagram illustrates a fluidic device for miniaturizing a Cas reactioncoupled with the enzyme invertase. Surface modification and readoutprocesses are depicted in exploded view schemes at the bottom including(a) optical readout using DNS, or other compound and (b) electrochemicalreadout (electrochemical analyzer or glucometer).

FIG. 14A shows for detecting a target nucleic acid in sample of patienturine. First, RNA is extracted from the urine sample. Then the extractedurine undergoes a pre-amplification step in which the target nucleicacid is amplified. The amplicons are then contacted to Cas13 complexedwith a guide nucleic that binds to the amplicons, which initiatescleavage of a detector nucleic acid comprising a fluorophore attached toa quencher by a nucleic acid. Upon cleavage of the detector nucleicacid, the fluorophore is detected as a positive signal, indicating thepresence of the target nucleic acid in the sample of patient urine.

FIG. 14B shows detection of prostate cancer RNA biomarkers using theworkflow of FIG. 14A, except the sample is from a prostate cell cancerline. The y-axis is background fluorescence (AU) and the x-axisindicates the detection of different prostate cancer RNA biomarkers(e.g., RNA #1, RNA #2, and RNA #3). Each RNA was detected in theprostate cancer cell line as indicated by the fluorescence. The sameworkflow and reagents were applied to a water sample and a samplecomprising RNA from a cervical cancer cell line, which were negativecontrols and showed little to no fluorescence indicating target nucleicacids encoding the prostate cancer RNA biomarkers were not present inthe samples as expected.

FIG. 14C shows that the fluorescence output as detected for eachprostate cancer RNA biomarker in FIG. 14B is a linear function of theconcentration of the target nucleic acid comprising encoding theprostate cancer RNA biomarker.

FIG. 15 shows SNP detection using Cas12a with a blue-eye guide nucleicacid or a brown-eye guide nucleic acid in saliva samples from blue-eyedand brown-eyed individuals, which were spatially multiplexed.Amplification of the HERC2 gene from human genomic DNA was conducted byPCR for 20 minutes followed by incubation for 30 minutes with the guideRNA complexed with Cas12a in a 20 μl assay volume. Fluorescence wasdetected using a plate reader for each sample. Seven volunteer subjectswere tested. The brown eye allele of the HERC2 gene was detected in fourof the volunteers. The blue eye allele of HERC2 gene was detected infive of the volunteers. Volunteers with both brown and blue eye allelesdetected were heterozygotes of the HERC2 gene, but displayed thedominant brown eye color. Of the fourteen tests conducted on the sevenvolunteer samples, seven were found to true positive, seven were foundto be true negative, zero were found to be false positive, and zero werefound to be false negative.

FIGS. 16A-16E illustrate detection of the alcohol flush SNP.

FIG. 16A illustrates that the workflow for the alcohol flush (ALDH2) SNPdetection. A saliva sample is taken from a subject and processed todetermine the genotype of the subject.

FIG. 16B shows alcohol flush (ALDH2) SNP detection using Cas12a with aguide nucleic acid for the G-SNP or a guide nucleic acid for the A-SNPin saliva samples from three volunteer subjects, which were spatiallymultiplexed. Amplification of the ALDH2 gene from human genomic DNA wasconducted by PCR followed by incubation with each guide RNA complexedwith Cas12a in 20 μl assay volumes. Fluorescence was detected using aplate reader for each sample. Both the G-SNP and A-SNP were detected inthe sample from volunteer #1. Only the G-SNP was detected in the samplesfrom volunteer #2 and volunteer #3.

FIG. 16C illustrates the genotype/phenotype correlation for the ALDH2SNP genotypes.

FIG. 16D shows the genotypes of each volunteer by sequencing (SEQ ID NOS180, 181, 180 and 180. respectively, in order of appearance), whichconfirms the genotype detected in FIG. 16B using Cas12a.

FIG. 16E is a table summarizing the parameters of FIG. 16B. TAT: turnaround time.

FIG. 17A illustrates the workflow for the exemplary syndromic panelidentification of sepsis of FIG. 17B. The workflow on the left shows aninput of mixed bacterial species that comprise the target nucleic acidsfor detection. DNA is extracted from these bacterial species, the targetDNA is amplified, and Cas12a complexed to guide RNAs for the targetnucleic acids for detection using spatial multiplexing. The binding ofthe target nucleic acids to the Cas12a complexed to guide RNAs for thetarget nucleic acids initiates cleavage of a detector nucleic acidcomprising a fluorophore attached to a quencher by a nucleic acid. Uponcleavage of the detector nucleic acid, the fluorophore is detected as apositive signal indicating the presence of the bacterial speciescomprising the target nucleic acids. The workflow on the right shows aninput of mixed bacterial species that lack the bacterial species fordetection. DNA is extracted from these bacterial species, the DNA isamplified and contacted to Cas12a complexed to guide RNAs for the targetnucleic acids for detection using spatial multiplexing. The lack ofbinding of target nucleic acids due to the absence of the target nucleicacids to the Cas12a complexed to guide RNAs for the target nucleic acidsdue to the absence of the target nucleic acids fails to initiatecleavage of a detector nucleic acid comprising a fluorophore attached toa quencher by a nucleic acid. Due to the lack of cleavage of thedetector nucleic acid, the fluorophore remains quenched in the intactdetector nucleic acid resulting in a negative signal indicating theabsence of bacterial species comprising the target nucleic acids.

FIG. 17B illustrates an exemplary test panel comprising 6 gram positiveand 4 gram negative bacterial pathogens from samples of purified genomicDNA benchmarked to pre-blood culture concentrations that underwent theworkflow as shown on the right side of FIG. 17A. The extracted DNA wasamplified by PCR and incubated with guide RNA complexed with Cas12a in20 μl assay volumes, in which the guide RNA bind to the target nucleicacid from the bacterial pathogens. Fluorescence was detected using aplate reader for each sample. The right panel shows that fluorescencewas detected for each bacterial pathogen. The turnaround time was 2.5hours.

FIG. 18A shows Cas13 and Cas12 multiplexing for detection of a bacteria.Cas13 is used for species detection of the bacteria. Cas12 is used todetect a mutation in a locus of the bacteria that confers antibioticresistance.

FIG. 18B shows a one-pot Cas13a and Cas12a detection coupled withisothermal amplification for detection of gonorrhea. Nucleic acids froma gonorrhea sample were incubated with Cas13a complexed to guide RNAsfor the species (gonorrhea) target nucleic acid for detection of thebacteria species and were incubated with Cas12a complexed to guide RNAsfor the antibiotic resistance allele target nucleic acid for detectionof the antibiotic resistance allele, using multiplexing. The binding ofthe gonorrhea target nucleic acids to the Cas13a complexed to guide RNAsfor the species target nucleic acids initiates cleavage of a detectornucleic acid comprising a fluorophore attached to a quencher by anucleic acid. Upon cleavage of the detector nucleic acid, thefluorophore was detected as shown in the graph, indicating gonorrhea waspresent in the sample. Similarly, the binding of the antibioticresistance allele target nucleic acids to the Cas12a complexed to guideRNAs for the antibiotic resistance allele target nucleic acids initiatescleavage of a detector nucleic acid comprising a fluorophore attached toa quencher by a nucleic acid. Upon cleavage of the detector nucleicacid, the fluorophore was detected as shown in the graph, indicating theantibiotic resistance allele was present in the sample. Samples withchlamydia and water were also tested using the same protocol, and asexpected, no fluorescence was detected for either sample.

FIG. 19 shows a comparison of detection for Chlamydia in 33 patientsamples using either qPCR or amplification paired with a CRISPR enzymeto detect a Chlamydia target nucleic acid.

FIG. 20A shows a cyclic voltammogram showing potential (V) on the x-axisversus current (μA) on the y-axis for the reporter only versus a cleavedreporter.

FIG. 20B shows a square wave voltammogram showing potential (V) on thex-axis versus current (μA) on the y-axis for the reporter only versus acleaved reporter.

FIG. 21A shows a graph of time in min on the x-axis versus fluorescence(AU) on the y-axis. The graph shows the real-time measurement offluorescence from a one-pot RT-RTA-IVT-DETECTR reaction carried out onchip.

FIG. 21B shows images of the entire microfluidic chip used for theDETECTR reactions depicted in FIG. 21A under an E-GEL transilluminator.Shown at left is time 0 and shown at right is at time of 35 min.

FIG. 21C shows a photograph of the prototype set-up (left image infigure) of the fluorescence-based readout for the on-chip, one-potDETECTR reaction of this example, a breadboard prototype (top rightimage in figure), and a fluorescence image of eppendorf tubes containingthe reaction at 30 minutes (bottom right image in figure).

FIG. 22A shows a panel of gRNAs for RSV evaluated for detectionefficiency. Darker squares in the background subtracted row indicategreater efficiency of detecting RSV target nucleic acids.

FIG. 22B shows graphs of pools of gRNA versus background subtractedfluorescence.

FIG. 23A shows a plate reader image of a results summarized in TABLE 8.

FIG. 23B shows the plate layout corresponding to FIG. 23A.

FIG. 24A shows a plate reader image of a results summarized in TABLE 9.

FIG. 24B shows the plate layout corresponding to FIG. 24A.

FIG. 25 shows that the functional range for the Type V protein Cas12M08(a variant within the Cas12 family having a sequence of SEQ ID NO: 155is between 25° C. and 45° C., with maximal activity at 35° C.

FIG. 26 shows the results of incubating Cas12 proteins for 15 minutes at45° C., 50° C., 55° C., 60° C., 65° C., or 70° C. and then decreasingthe reaction temperature to 37° C.

FIG. 27 shows that the stability of Cas12M08 at elevated temperatures isdependent on the buffer composition.

FIG. 28 shows individual parts of sample preparation devices of thepresent disclosure. FIG. 28A of the figure shows a single chamber sampleextraction device. FIG. 28B shows filling the dispensing chamber withmaterial that further purifies the nucleic acid as it is dispensed is anoption. FIG. 28C shows options for the reaction/dispensing chamber.

FIG. 29 shows a sample work flow using a sample processing device.

FIG. 30 shows extraction buffers used to extract Influenza A RNA fromremnant clinical samples.

FIG. 31 shows that low pH conditions allow for rapid extraction ofInfluenza A genomic RNA.

FIG. 32 shows the application of RT-RPA to the detection of Influenza A,Influenza B, and human Respiratory Syncytial Virus (RSV) viral RNA byCas12a. The schematic at left shows the workflow including providingDNA/RNA, RPA/RT-RPA, and Cas12a detection. The graphs at right show theresults of Cas12a detection as measured by fluorescence over time.

FIG. 33 shows the application of RT-RPA coupled with an IVT reactionenabling detection of viral RNA using Cas13a. The schematic at leftshows the workflow including providing DNA/RNA, RPA/RT-RPA, in vitrotranscription, and Cas13a detection. The graph at right shows theresults of Cas13a detection as measured by fluorescence for each testedcondition.

FIG. 34 shows the production of RNA, as detected by Cas13a, from an RNAvirus using an RT-RPA-IVT “two-pot” reaction. The schematic at leftshows the workflow including providing DNA/RNA, RPA/RT-RPA and in vitrotranscription in a first reaction, and Cas13a detection in a secondreaction. The graph at right shows the results of Cas13a detection asmeasured by fluorescence for each tested condition.

FIG. 35 shows the effect of various buffers on the performance of aone-pot Cas13a assay. The schematic at left shows the workflow includingproviding DNA/RNA and RPA/RT-RPA, in vitro transcription, and Cas13adetection. The graph at right shows the results of Cas13a detection asmeasured by fluorescence for each tested condition.

FIG. 36 shows the specific detection of viral RNA from the Peste despetits ruminants (PPR) virus that infects goats using the one-pot Cas13aassay. The schematic at left shows the workflow including providingDNA/RNA and RPA/RT-RPA, in vitro transcription, and Cas13a detection.The graphs at right show the results of Cas13a detection as measured byfluorescence over time for the tested conditions.

FIG. 37 shows the specific detection of Influenza B using the one-potCas13a assay run at 40° C. 40 fM of viral RNA was added to the reaction.The schematic at left shows the workflow including providing DNA/RNA andRPA/RT-RPA, in vitro transcription, and Cas13a detection. The graphs atright show the results of Cas13a detection as measured by fluorescencefor each tested condition.

FIG. 38 shows the tolerance of the one-pot Cas13a assay for thedetection of RNA from the Influenza B virus in the presence and in theabsence of a universal viral transport medium called universal transportmedia (UTM Copan) at 40° C. The schematic at left shows the workflowincluding providing DNA/RNA and RPA/RT-RPA, in vitro transcription, andCas13a detection. The graphs at right show the results of Cas13adetection over time for each tested condition.

FIG. 39 shows the one-pot Cas13a detection assay at varioustemperatures.

FIG. 39A shows a schematic of the workflow including providing DNA/RNAand the one-pot reaction including RPA/RT-RPA, in vitro transcription,and Cas13a detection.

FIG. 39B shows a graph of Cas13a detection of Influenza A RNA at varioustemperatures.

FIG. 39C shows a graph of Cas13a detection of Influenza B RNA at varioustemperatures.

FIG. 39D shows a graph of Cas13a detection of human RSV (FIG. 39D) RNAat various temperatures.

FIGS. 40A-C shows the optimization of a LAMP reaction for the detectionof an internal amplification control using a DNA sequence derived fromthe Mammuthus primigenius (Wooly Mammoth) mitochondria.

FIG. 40A shows a schematic of the workflow including providing DNA/RNA,LAMP/RT-LAMP, and Cas12a detection.

FIG. 40B shows the time to result for LAMP reactions for an internalamplification control using a DNA sequence derived from the Mammuthusprimigenius, as quantified by fluorescence.

FIG. 40C shows Cas12a specific detection at 37° C. of LAMP amplicon fromthe 68° C. temperature reaction.

FIGS. 41A-C shows the optimization of LAMP and Cas12 specific detectionof the human POP7 gene that is a component of RNase P.

FIG. 41A shows a schematic of the workflow including providing DNA/RNA,LAMP/RT-LAMP, and Cas12a detection.

FIG. 41B shows the time to result of a LAMP/RT-LAMP reaction for RNase PPOP7 at different temperatures, as quantified by fluorescence.

FIG. 41C shows three graphs demonstrating Cas12a specific detection at37° C. of LAMP/RT-LAMP amplicon from the 68° C. temperature reaction.

FIG. 42 shows the specific detection of three different RT-LAMPamplicons for Influenza A virus. At left is a schematic of the workflowincluding providing DNA/RNA, LAMP/RT-LAMP, and Cas12a detection. Atright are graphs showing the results of Cas12a detection as measured byfluorescence over time for each tested condition.

FIG. 43 shows the identification of optimal crRNAs for the specificdetection of Influenza B (IBV) RT-LAMP amplicons. At left is a schematicof the workflow including providing DNA/RNA, LAMP/RT-LAMP, and Cas12adetection. At right are graphs showing the results of Cas12a detectionas measured by fluorescence over time for each tested condition (IAV isinfluenza A virus, IBV is influenza B virus, NTC is no templatecontrol).

FIG. 44 shows the results of the 1% agarose gel with bands showing theproducts of the RT-LAMP reaction.

FIG. 45 shows Cas12a discrimination between amplicons from a multiplexRT-LAMP reaction for Influenza A and Influenza B.

FIG. 45A shows a schematic of the workflow including providing viralRNA, multiplexed RT-LAMP, and Cas12a influenza A detection or Cas12ainfluenza B detection.

FIG. 45B shows Cas12a detection of RT-LAMP amplicons after 30 minutemultiplexed RT-LAMP amplification at 60° C.

FIG. 45C shows background subtracted fluorescence at 30 minutes ofCas12a detection at 37° C. of RT-LAMP amplicons for 10,000 viral genomecopies of IAV and IBV.

FIG. 46 shows Cas12a discrimination between a triple multiplexed RT-LAMPreaction for Influenza A, Influenza B, and the Mammuthus primigenius(Wooly Mammoth) mitochondria internal amplification control sequenceafter 30 minutes of multiplexed RT-LAMP amplification at 60° C. At topis a schematic of the worrkflow including providing viral RNA,multiplexed RT-LAMP, and Cas12a influenza A detection or Cas12ainfluenza B detection or Cas12 internal amplification control detection.At bottom are graphs showing the results of Cas12 detection as measuredby fluorescence over time for each tested condition.

FIG. 47 shows schematics of LAMP and RT-LAMP primer designs.

FIGS. 47A-B shows that a T7 promoter can be included on the F3 or B3primers (outer primers), or FIP or BIP primers for Influenza A.

FIG. 47A shows a schematic illustrating the identity of the primers usedin LAMP and RT-LAMP. Primers LF and LB are option in some LAMP andRT-LAMP designs, but generally increase the efficiency of the reaction.

FIG. 47B shows a schematic illustrating the position and orientation ofthe T7 promoter in a variety of LAMP primers.

FIG. 48A shows a schematic of the workflow including providing DNA/RNA,LAMP/RT-LAMP, in vitro transcription, and Cas13a detection.

FIG. 48B shows the time to result for RT-LAMP reactions for Influenza Ausing different primer sets, as quantified by fluorescence.

FIG. 48C shows in vitro transcription (IVT) with T7 RNA polymerase ofthe product of the RT-LAMP reactions for Influenza A using differentprimer sets at 37° C. for 10 minutes.

FIG. 49 shows the detection of a RT-SIBA amplicon for Influenza A byCas12. At left is a schematic of the workflow including providingDNA/RNA, SIBA/RT-SIBA, and Cas12a detection. At right is a graph showingCas12a detection as measured by fluorescence for each of the testedconditions.

FIG. 50 shows graphs of activity, as measured by fluorescence, with(left graph) and without (right graph) activator over time.

FIGS. 51A-B shows inhibition of Cas13a activity by SDS and urea.

FIG. 51A shows the Cas13a detection assay performed in the presence of0-200 mM urea.

FIG. 51B shows complete inhibition of Cas13a upon addition of 0.1% orgreater amounts of SDS to the reaction (left graph shows with activatorand right graph shows without activator).

FIGS. 52A-B shows the performance of Cas13a in DETECTR reactions withvarying concentrations of salt.

FIG. 52A shows the results of varying the concentration of NaCl in aCas13a DETECTR reaction.

FIG. 52B shows the results of varying the concentration of KCl in aCas13a DETECTR reaction.

FIGS. 53A-B shows optimization of DTT concentration in a Cas13a DETECTRassay.

FIG. 53A shows varying DTT concentration in NaCl.

FIG. 53B shows varying DTT concentrations in KCl. The orange barindicates original buffer conditions (50 mM KCl) and no DTT.

FIG. 54A-54B show the activity of Cas13a in the DETECTR assay, asmeasured by fluorescence, for each of the tested reporters.

FIG. 55A-55B show Cas13a activity in the DETECTR assay, as measured byfluorescence, for each of the tested conditions.

FIG. 56A-56B show Cas13a performance in the DETECTR assay, as measuredby fluorescence, for each of the five commercially available buffers andthe original HEPES pH 6.8 buffer.

FIG. 57 shows a head-to-head comparison of the original HEPES pH 6.8buffer to the optimized MBuffer1 for a Cas13a DETECTR assay withserially diluted target RNAs and run at 37° C. for 30 minutes.

FIG. 58 shows that 5% glycerol in MBuffer1 (left graph) increases assayperformance in comparison to an identical buffer without glycerol (rightgraph).

FIG. 59 shows a gradient chart of Cas13a activity in the DETECTR assay,as measured by fluorescence, (darker squares indicate increased Cas13aactivity) versus varying NP-40 concentration along the x-axis andvarying BSA concentration along the y-axis.

FIG. 60A-60B show Cas13a performance in DETECTR assays, as measured byfluorescence, versus the different additives tested.

FIG. 61A-61B show the results of screening 84 different buffer and pHcombinations to determine the optimal buffer for Lba-Cas12a activity inDETECTR assays, as measured by fluorescence.

FIG. 62 shows Lba-Cas12a performance in DETECTR assays, as measured byfluorescence, in each of the tested conditions.

FIG. 63A-63B show Cas12M08 performance in DETECTR assays, as measured byfluorescence, for each of the tested conditions (buffer type and pH).

FIG. 64 shows Cas12M08 performance in DETECTR assays, as measured byfluorescence, for the various salt types and concentrations tested.

FIG. 65 shows Cas12M08 performance in DETECTR assays, as measured byfluorescence (darker squares indicate greater fluorescence and moreactivity), versus heparin concentration on the x-axis and KOAc bufferconcentration on the y-axis.

FIG. 66A-66 show that specific compounds inhibited the performance ofthe assay including: benzamidine hydrochloride, beryllium sulfate,manganese chloride, potassium bromide, sodium iodine, zinc chloride,di-ammonium hydrogen phosphate, tri-lithium citrate, tri-sodium citrate,cadmium chloride, copper chloride, yttrium chloride, 1-6 diaminohexane,1-8-diaminooctane, ammonium fluoride, and ammonium sulfate.

FIG. 67 shows the results of evaluating SNP sensitivity along targetsequences for Cas12M08.

FIG. 68 shows the results of evaluating SNP sensitivity along targetsequences for Lba-Cas12a.

FIG. 69A shows a photograph of test strips, which from left to rightshow Lba-Cas12a with target, Lba-Cas12a without target, Cas12M08 withtarget, and Cas12M08 without target.

FIG. 69B shows a graph of fluorescence on the y-axis for each grouptested (Lba-Cas12a with target, Lba-Cas12a without target, Cas12M08 withtarget, and Cas12M08 without target).

FIG. 69C shows a photograph of various test strips from Cas13M DETECTRassays with 10 nM, 1 nM, 0.1 nM, 0.01 nM, target DNA or no target DNA.

FIG. 70 shows the layout of a Milenia commercial strip with a typicalreporter.

FIG. 71 shows the layout of a Milenia HybridDetect 1 strip with anamplicon.

FIG. 72 shows the layout of a Milenia HybridDetect 1 strip with astandard Cas reporter.

FIG. 73 shows a modified Cas reporter comprising a DNA linker tobiotin-dT (shown as a pink hexagon) bound to a FAM molecule (shown as agreen start).

FIG. 74 shows the layout of Milenia HybridDetect strips with themodified Cas reporter.

FIG. 75 shows an example of a single target assay format (to left) and amultiplexed assay format (to right).

FIG. 76 shows another variation of an assay prior to use (top), an assaywith a positive result (middle left), an assay with a negative result(middle right), and a failed test (bottom).

FIG. 77 shows one design of a tethered lateral flow Cas reporter.

FIG. 78 shows a workflow for CRISPR diagnostics using the tetheredcleavage reporter using magnetic beads.

FIG. 79A shows a FAM-biotin reporter conjugated to magnetic beads,further incubated in the presence or absence of TURBO DNase (Thermo) for15 minutes at 37C.

FIG. 79B shows a DIG-biotin reporter, which was conjugated to magneticbeads and incubated in the presence or absence of TURBO DNase (Thermo)for 15 minutes at 37C.

FIG. 79C shows a schematic of tethered cleavage reporters, which can beused to multiplex readouts fro CRISPR diagnostics (left), and two sampletest strips (right).

FIG. 80 shows photographs of test strips where a tethered cleavagereporter was released by CRISPR-Cas proteins.

FIG. 81 shows a schematic for an enzyme-reporter system that is filteredby streptavidin-biotin before reaching the reaction chamber.

FIG. 82 shows an invertase-nucleic acid used for the detection of atarget nucleic acid. The invertase-nucleic acid, immobilized on amagnetic bead, is added to a sample reaction containing Cas protein,guide RNA, and a target nucleic acid. Target recognition activates theCas protein to cleave the nucleic acid of the invertase-nucleic acid,liberating the invertase enzyme from the immobilized magnetic bead. Thissolution is either be transferred to the “reaction mix”, which containssucrose and the DNS reagent and changes color from yellow to red whenthe invertase converts sucrose to glucose or is can be transferred to ahand-held glucometer device for a digital readout.

FIGS. 83A-83C show example color change readout by invertase-nucleicacids in reaction mix. DNS reagent produces a colorimetric change wheninvertase converts sucrose to glucose. Free invertase at 0.4 or 4 uM wasreacted with 0-60 mM sucrose for 5, 10, 15 or 30 min at roomtemperature, and samples were heated at 95 C for 10 sec to enhance thecolor change.

FIG. 84 shows one layout for a DETECTR assay. In this layout a swabcollection cap seals a swab reservoir chamber. Clockwise to the swabreservoir chamber is a chamber holding the amplification reaction mix.Clockwise to the chamber holding the amplification reaction mix is achamber holding the DETECTR reaction mix. Clockwise to this is thedetection area. Clockwise to the detection area is the pH balance well.A cartridge wells cap is shown and seals all the wells containing thevarious reagent mixtures. The cartridge itself is shown as a squarelayer at the bottom of the schematic. To the right is a diagram of theinstrument pipers pump which drives the fluidics in each chamber/welland is connected to the entire cartridge. Below the cartridge is arotary valve that interfaces with the instrument.

FIG. 85 shows one workflow of the various reactions in the DETECTR assayof FIG. 84 . First, as shown in the top left diagram, a swab may beinserted into the 200 ul swab chamber and mixed. In the middle leftdiagram, the valve is rotated clockwise to the “swab chamber position”and 1 uL of sample is picked up. In the lower left diagram, the valve isrotated clockwise to the “amplification reaction mix” position and the 1ul of sample is dispensed and mixed. In the top right diagram, 2 uL ofsample is aspirated from the “amplification reaction mix”. In the topmiddle diagram, the valve is rotated clockwise to the “DETECTR”position, the sample is dispensed and mixed, and 20 ul of the sample isaspirated. Finally, in the bottom right diagram, the valve is rotatedclockwise to the detection area position and 20 ul of the sample isdispensed.

FIG. 86 shows a modification of the workflow shown in FIG. 85 that isalso consistent with the methods and systems of the present disclosure.At left is the diagram shown at the top right of FIG. 85 . At right isthe modified diagram in which there is a first amplification chambercounterclockwise to the swab lysis chamber and a second amplificationchamber clockwise to the swab lysis chamber. Additionally, clockwise toamplification chamber #2 are two sets, or “duplex”, DETECTR chamberslabeled “Duplex DETECTR Chambers #2” and “Duplex DETECTR Chambers #1”,respectively.

FIG. 87 shows breakdown of the workflow for the modified layout shown inFIG. 86 . Specifically, from the swab lysis chamber, which holds 200 ulof sample, 20 ul of the sample can be moved to amplification chamber #1and 20 ul of the sample can be moved to amplification chamber #2. Afteramplification in amplification chamber #1, 20 ul of the sample can bemoved to Duplex DETECTR Chambers #1 a and 20 ul of the sample can bemoved to Duplex DETECTR Chambers #1 b. Additionally, after amplificationin amplification chamber #2, 20 ul of the sample can be moved to DuplexDETECTR Chambers #2a and 20 ul of the sample can be moved to DuplexDETECTR Chambers #2b.

FIG. 88 shows the modifications to the cartridge illustrated in FIG. 86and FIG. 87 .

FIG. 89 shows a top down view of the cartridge of FIG. 88 . This layoutand workflow has a replicate in comparison to the layout and workflow ofFIGS. 84-85 .

FIG. 90 shows a layout for a DETECTR assay. Shown at top is a pneumaticpump, which interfaces with the cartridge. Shown at middle is a top downview of the cartridge showing a top layer with reservoirs. Shown atbottom is a sliding valve containing the sample and arrows pointing tothe lysis chamber at left, following by amplification chambers to theright, and DETECT chambers further to the right.

FIG. 91 shows a comparison of the DETECTR assays disclosed herein to thegold standard PCR-based method of detecting a target nucleic acid. Shownat top is a flow chart showing a gradient of sample prep evaluation fromcrude (left) to pure (right). Sample prep steps that take a crude sampleto a pure sample include lysis, binding, washing, and eluting. DETECTRassays disclosed herein may only need the sample prep step of lysis,yielding a crude sample. On the other hand, PCR-based methods canrequire lysis, binding, washing, and elution, yielding a very puresample. The graph at bottom shows that even with a cruder sample prep,the DETECTR assay disclosed herein can identify target nucleic acidsjust as well as gold standard PCR-based methods of detection.

FIG. 92 shows Cas13a detection of RT-LAMP DNA amplicon.

FIG. 92A shows a schematic of the workflow including providing DNA/RNA,LAMP/RT-LAMP, and Cas13a detection.

FIG. 92B shows Cas13a specific detection of RT-LAMP DNA amplicon with afirst primer set as measured by background subtracted fluorescence onthe y-axis.

FIG. 92C shows Cas13a specific detection of RT-LAMP DNA amplicon with asecond primer set as measured by background subtracted fluorescence onthe y-axis.

FIGS. 93A-C shows the results of Cas13 and Cas12 detection assays.

FIG. 93A shows a Cas13 detection assay using 2.5 nM RNA, single-strandedDNA (ssDNA), or double-stranded (dsDNA) as target nucleic acids, wheredetection was measured by fluorescence for each of the targets tested.

FIG. 93B shows Cas12 detection assay using 2.5 nM RNA, ssDNA, and dsDNAas target nucleic acids, where detection was measured by fluorescencefor each of the targets tested.

FIG. 93C shows the performance of Cas13 and Cas12 on RNA, ssDNA, anddsDNA targets at various concentrations, where detection was measured byfluorescence for each of the targets tested.

FIG. 94 shows an Lbu-Cas13a detection assay using 2.5 nM ssDNA targetwith 170 nM of various reporter substrates, wherein detection wasmeasured by fluorescence for each of the reporter substrates tested.

FIGS. 95A-B shows the results of Cas13 detection assays for Lbu-Cas13a.

FIG. 95A shows the results of Cas13 detection assays for Lbu-Cas13a andLwa-Cas13a using 10 nM or 0 nM of ssDNA target, where detection wasmeasured by fluorescence resulting from cleavage of reporters over time.

FIG. 95B shows the results of Cas13 detection assays for Lbu-Cas13a andLwa-Cas13a using 10 nM or 0 nM of ssDNA target, where detection wasmeasured by fluorescence resulting from cleavage of reporters over time.

FIG. 96 shows Lbu-Cas13a detection assay using 1 nM RNA (at left) orssDNA (at right) target in buffers with various pH values ranging from6.8 to 8.2.

FIGS. 97A-E shows guide RNAs (gRNAs) tiled along a target sequence andthe results of detection assays using the depicted gRNAs.

FIG. 97A shows guide RNAs (gRNAs) tiled along a target sequence at 1nucleotide intervals.

FIG. 97B shows Cas13M26 detection assays using 0.1 nM RNA or 2 nM ssDNAtarget with gRNAs tiled at 1 nucleotide intervals and an off-targetgRNA.

FIG. 97C shows data from FIG. 97B ranked by performance of ssDNA.

FIG. 97D shows performance of gRNAs on RNA split by the identity of thenucleotide on the target that is 3′ of the target sequence.

FIG. 97E shows performance of gRNAs on RNA split by the identity of thenucleotide on the target that is 3′ of the target sequence.

FIGS. 98A-B shows the results of Lbu-Cas13a and Cas13M26 detectionassays.

FIG. 98A shows Lbu-Cas13a detection assays using 1 μL of DNA ampliconfrom various LAMP isothermal nucleic acid amplification reactions.

FIG. 98B shows Cas13M26 detection assays using various amounts of PCRreaction as a DNA target.

FIG. 99 illustrates a DNS sucrose reaction with invertase-conjugated DNAoligos.

FIGS. 100A-B shows a pneumatic valve device layout for a DETECTR assay.

FIG. 100A shows a schematic of a pneumatic valve device. A pipette pumpaspirates and dispenses samples. An air manifold is connected to apneumatic pump to open and close the normally closed valve. Thepneumatic device moves fluid from one position to the next. Thepneumatic design has reduced channel cross talk compared to other devicedesigns.

FIG. 100B shows a schematic of a cartridge for use in the pneumaticvalve device shown in FIG. 100A. The valve configuration is shown. Thenormally closed valves (one such valve is indicated by an arrow)comprise an elastomeric seal on top of the channel to isolate eachchamber from the rest of the system when the chamber is not in use. Thepneumatic pump uses air to open and close the valve as needed to movefluid to the necessary chambers within the cartridge.

FIG. 101 shows a valve circuitry layout for the pneumatic valve device.A sample is placed in the sample well while all valves are closed, asshown at (i.). The sample is lysed in the sample well. The lysed sampleis moved from the sample chamber to a second chamber by opening thefirst quake valve, as shown at (ii.), and aspirating the sample usingthe pipette pump. The sample is then moved to the first amplificationchamber by closing the first quake valve and opening a second quakevalve, as shown at (iii.) where it is mixed with the amplificationmixture. After the sample is mixed with the amplification mixture, it ismoved to a subsequent chamber by closing the second quake valve andopening a third quake valve, as shown at (iv). The sample is moved tothe DETECTR chamber by closing the third quake valve and opening afourth quake valve, as shown at (v). The sample can be moved through adifferent series of chambers by opening and closing a different seriesof quake valves, as shown at (vi). Actuation of individual valves in thedesired chamber series prevents cross contamination between channels.

FIG. 102 shows a schematic of a sliding valve device. The offset pitchof the channels allows aspirating and dispensing into each wellseparately and helps to mitigate cross talk between the amplificationchambers and corresponding chambers.

FIG. 103 shows a diagram of sample movement through the sliding valvedevice shown in FIG. 102 . In the initial closed position (i.), thesample is loaded into the sample well and lysed. The sliding valve isthen actuated by the instrument, and samples are loaded into each of thechannels using the pippette pump, which dispenses the appropriate volumeinto the channel (ii.). The sample is delivered to the amplificationchambers by actuating the sliding valve and mixed with the pipette pump(iii.). Samples from the amplification chamber are aspirated into eachchannel (iv.) and then dispensed and mixed into each DETECTR chamber(v.) by actuating the sliding valve and pipette pump.

FIG. 104 illustrates a method of removing ssDNA from a type Vprogrammable nuclease DETECTR reaction following target amplification. Atarget nucleic acid is amplified using PCR, allele-specific PCR, orisothermal amplification. The amplification process results in a mixtureof dsDNA and ssDNA products. A ssDNase 3′ to 5′ exonuclease I,exonuclease III, exonulcease T, or RecJf is added to the amplifiedtarget nucleic acid sample. The ssDNase degrades ssDNA, leaving onlydsDNA products. The presence of a SNP of interest in the target dsDNA isthen detected using a type V SNP DETECTR reaction.

FIG. 105 shows the raw fluorescence produced in each well containing aCas12a complexing reaction with different volumes of LAMP ampliconproduct. A higher fluorescence value is indicative of better assayperformance. Addition of 2 μL of LAMP amplicon per DETECTR reactionshowed the best assay performance (highest fluorescence) of any of theconditions tested. Increasing volumes of LAMP amplicon resulted in adecreasing assay performance, as measured by fluorescence.

FIG. 106 shows a schematic of the top layer of a cartridge of apneumatic valve device of the present disclosure, highlighting suitabledimensions. The schematic shows one cartridge that is 2 inches by 1.5inches.

FIG. 107 shows a schematic of a modified top layer of a cartridge of apneumatic valve device of the present disclosure adapted forelectrochemical dimension. In this schematic, three lines are shown inthe detection chambers (4 chambers at the very right). These three linesrepresent wiring (or “metal leads”), which is co-molded, 3D-printed, ormanually assembled in the disposable cartridge to form a three-electrodesystem.

DETAILED DESCRIPTION

Described herein are devices, systems, fluidic devices, kits, andmethods for detecting the presence of a target nucleic acid in a sample.The devices, systems, fluidic devices, kits, and methods for detectingthe presence of a target nucleic acid in a sample can be used in a rapidtest (e.g., lab test or point-of-care test) for detection of a targetnucleic acid of interest. For example, disclosed herein are particularmicrofluidic devices, lateral flow devices, sample preparation devices,and compositions (e.g., programmable nucleases, guide RNAs, reagents forin vitro transcription, reagents for amplification, reagents for reversetranscription, reporters, or any combination thereof) for use in saiddevices that are particularly well suited for carrying out a highlyefficient, rapid, and accurate reactions for detecting whether a targetnucleic acid is present in a sample. In particular, provided herein aredevices, systems, fluidic devices, and kits, wherein the rapid tests canbe performed in a single system. The target nucleic acid may be aportion of a nucleic acid of interest, e.g., a target nucleic acid fromany plant, animal, virus, or microbe of interest.

A device, system, fluidic device, or kit for rapid tests, as describedherein, may comprise reagents for the detection of a target nucleic acidusing a programmable nuclease. The device, system, fluidic device, orkit for rapid tests may enable monitoring and visualization of a targetnucleic acid in a sample. For example, reagents disclosed herein (e.g.,programmable nucleases, guide RNAs, reagents for in vitro transcription,reagents for amplification, reagents for reverse transcription, andreporters, or any combination thereof) are particularly well suited foruse in a device described herein to carry out highly efficient, rapid,and accurate reactions for detecting whether a target nucleic acid ispresent in a sample. A device described herein may include a particularmicrofluidic device (e.g., a pneumatic valve device, a sliding valvedevice, or a rotating valve device), a lateral flow device, or a samplepreparation device. In some embodiments, the method for use of thedevice, system, fluidic device, or kit for rapid tests may comprise someor all of the steps of sample preparation, nucleic acid amplification,programmable nuclease reaction incubation, and detection or readout.

Various ailments, such as communicable disease, cancer, and geneticdisorders, may have poor outcomes, including severe symptoms that canlead to death. The capability to quickly and accurately detect thepresence of an ailment can provide valuable information and lead toactions to reduce the progression or transmission of the ailment.

The devices, systems, fluidic devices, kits, and methods for detectingthe presence of a target nucleic acid in a sample are advantageous fordetecting a target nucleic acid comprising a particular genotype orassociated with particular phenotype, such as detection of a targetnucleic acid associated with a communicable disease. Variouscommunicable diseases can easily spread from an individual orenvironment to an individual. Individuals with one or more of thesediseases may have poor outcomes, including severe symptoms that can leadto death. The detection of the disease in an individual, especially atthe early stages of the disease, may provide guidance on treatments orinterventions to reduce the progression of the disease. Additionally,the detection of traits of the disease, such as resistance to anantibiotic, can be useful for informing treatment of the disease. Thedetection of the disease in the environment may provide guidance oninterventions to reduce or minimize a potential epidemic or transmissionof the disease. The capability to quickly and accurately detect thepresence of a disease in a biological or environmental sample canprovide valuable information and lead to actions to reduce thetransmission of the disease.

Additionally, early detection of cancers and genetic disorders can beimportant for initiating treatment. Individuals with cancer or geneticdisorders may have poor outcomes, including severe symptoms that canlead to death, if left undetected. The detection of the cancer orgenetic disorder in an individual, especially at the early stages of thecancer or genetic disorder, may provide guidance on treatments orinterventions to reduce the progression of the cancer or maladiesassociated with progression of the genetic disorder.

The present disclosure provides various devices, systems, fluidicdevices, and kits for rapid tests, which may quickly assess whether atarget nucleic acid is present in a sample by using a programmablenuclease that can interact with functionalized surfaces of the fluidicsystems to generate a detectable signal. For example, disclosed hereinare particular microfluidic devices, lateral flow devices, samplepreparation devices, and compositions (e.g., programmable nucleases,guide RNAs, reagents for in vitro transcription, amplification, reversetranscription, and reporters, or any combination thereof) for use insaid devices that are particularly well suited to carry out a highlyefficient, rapid, and accurate reactions for detecting the presence of atarget nucleic acid (e.g., a DETECTR reaction). The systems andprogrammable nucleases disclosed herein can be used as a companiondiagnostic with any of the diseases disclosed herein (e.g., RSV, sepsis,flu), or can be used in reagent kits, point-of-care diagnostics, orover-the-counter diagnostics. The systems may be used as a point of carediagnostic or as a lab test for detection of a target nucleic acid and,thereby, detection of a condition, for example, in a subject from whichthe sample was taken. The systems may be used in various sites orlocations, such as in laboratories, in hospitals, in physicianoffices/laboratories (POLs), in clinics, at remotes sites, or at home.Sometimes, the present disclosure provides various devices, systems,fluidic devices, and kits for consumer genetic use or for over thecounter use.

Furthermore, detection of a target nucleic acid for determining geneticinformation is consistent with the methods devices, systems, fluidicdevices, kits, and methods described herein. A target nucleic acid fordetermining genetic information can include, but is not limited to, anucleic acid associated with organism ancestry (e.g., a nucleic acidcomprising a single nucleotide polymorphism that identifies geographicalancestry, ancestry from an ethnic group, etc.); a nucleic acid for traitnot associated with a communicable disease, cancer, or genetic disorder;a nucleic acid for a phenotypic trait (e.g., a nucleic acid from a genefor blue eyes, brown hair color, fast or slow metabolism of a drug suchas caffeine, an intolerance such as lactose intolerance, etc.), or anucleic acid for genotyping (e.g., a nucleic acid for a gene that isrecessive, such as the gene for Taye-Sachs disease).

Described herein are devices, systems, fluidic devices, kits, andmethods for detecting the presence of a target nucleic acid in a sample.The devices, systems, fluidic devices, kits, and methods for detectingthe presence of a target nucleic acid in a sample can be used in a rapidtest (e.g., lab test or point-of-care test) for detection of a targetnucleic acid of interest. For example, disclosed herein are particularmicrofluidic devices, lateral flow devices, sample preparation devices,and compositions (e.g., programmable nucleases, guide RNAs, reagents forin vitro transcription, reagents for amplification, reagents for reversetranscription, reporters, or any combination thereof) for use in saiddevices that are particularly well suited to carrying out a highlyefficient, rapid, and accurate for detecting whether a target nucleicacid is present in a sample (e.g., a DETECTR reaction). In particular,provided herein are devices, systems, fluidic devices, and kits, whereinthe rapid tests can be performed in a single system. The target nucleicacid may be a portion of a nucleic acid from a virus or a bacterium orother agents responsible for a disease in the sample. The target nucleicacid may be a portion of a nucleic acid from a gene expressed in acancer or genetic disorder in the sample. The target nucleic acid may bea portion of an RNA or DNA from any organism in the sample. In someembodiments, programmable nucleases disclosed herein are activated toinitiate trans cleavage activity of an RNA reporter by RNA or DNA. Asused herein, “trans cleavage” is used interchangably with “collateralcleavage.” A programmable nuclease as disclosed herein is, in somecases, binds to a target RNA to initiate trans cleavage of an RNAreporter, and this programmable nuclease can be referred to as anRNA-activated programmable RNA nuclease. In some instances, aprogrammable nuclease as disclosed herein binds to a target DNA toinitiate trans cleavage of an RNA reporter, and this programmablenuclease can be referred to as a DNA-activated programmable RNAnuclease. In some cases, a programmable nuclease as described herein iscapable of being activated by a target RNA or a target DNA. For example,a Cas13, such as Cas13a, disclosed herein is activated by a target RNAnucleic acid or a target DNA nucleic acid to transcollaterally cleaveRNA reporter molecules. In some embodiments, the Cas13 binds to a targetssDNA which initiates trans cleavage of RNA reporters. In someinstances, a programmable nuclease as disclosed herein binds to a targetDNA to initiate trans cleavage of a DNA reporter, and this programmablenuclease can be referred to as a DNA-activated programmable DNAnuclease.

The programmable nuclease can become activated after binding of a guidenucleic acid with a target nucleic, in which the activated programmablenuclease can cleave the target nucleic acid and can have trans cleavageactivity. Trans cleavage activity can be non-specific cleavage of nearbysingle-stranded nucleic acids by the activated programmable nuclease,such as trans cleavage of detector nucleic acids with a detectionmoiety. Once the detector nucleic acid is cleaved by the activatedprogrammable nuclease, the detection moiety can be released or separatedfrom the reporter and generates a detectable signal that is immobilizedon a support medium. Often the detection moiety is at least one of afluorophore, a dye, a polypeptide, or a nucleic acid. Sometimes thedetection moiety binds to a capture molecule on the support medium to beimmobilized. The detectable signal can be visualized on the supportmedium to assess the presence or level of the target nucleic acidassociated with an ailment, such as a disease, cancer, or geneticdisorder. The programmable nuclease can be a CRISPR-Cas (clusteredregularly interspaced short palindromic repeats—CRISPR associated)nucleoprotein complex with trans cleavage activity, which can beactivated by binding of a guide nucleic acid with a target nucleic acid.

The reporter molecules can be RNA reporter molecules, wherein the RNAreporter molecule comprises at least one ribonucleic acid and adetectable moiety. In some embodiments, the Cas13a recognizes anddetects ssDNA and, further, specifically trans-cleaves RNA reporters.The detection of the target nucleic acid in the sample may indicate thepresence of the disease in the sample and may provide information fortaking action to reduce the transmission of the disease to individualsin the disease-affected environment or near the disease-carryingindividual. The detection of the target nucleic acid in the sample mayindicate the presence of a disease mutation, such as a single nucleotidepolymorphism (SNP) that provides antibiotic resistance to adisease-causing bacteria. The detection of the target nucleic acid inthe sample may indicate the presence of the cancer or genetic disorderin the sample and may provide information for treating or slowingprogression of the cancer or genetic disorder. The detection of thetarget nucleic acid is facilitated by a programmable nuclease.

A device, system, fluidic device, or kit for rapid tests, as describedherein, may comprise reagents for the detection of a target nucleic acidusing a programmable nuclease. The device, system, fluidic device, orkit for rapid tests may enable monitoring and visualization of a targetnucleic acid in a sample. For example, reagents disclosed herein (e.g.,programmable nucleases, guide RNAs, reagents for in vitro transcription,reagents for amplification, reagents for reverse transcription, andreporters, or any combination thereof) are particularly well suited foruse in a device described herein to carry out highly efficient, rapid,and accurate for detecting the presence of a target nucleic acid (e.g.,a DETECTR reaction). A device described herein may include a particularmicrofluidic device (e.g., a pneumatic valve device, a sliding valvedevice, or a rotating valve device), a lateral flow device, or a samplepreparation device. In some embodiments, the method for use of thedevice, system, fluidic device, or kit for rapid lab tests may comprisesome or all of the steps of sample preparation, nucleic acidamplification, programmable nuclease reaction incubation, and detectionor readout.

In one aspect, described herein, is a system for detecting a targetnucleic acid. The system may comprise a support medium; a guide nucleicacid targeting a target sequence; a programmable nuclease capable ofbeing activated when complexed with the guide nucleic acid and thetarget sequence; and a single stranded detector nucleic acid comprisinga detection moiety, wherein the detector nucleic acid is capable ofbeing cleaved by the activated nuclease, thereby generating a firstdetectable signal.

In another aspect, described herein is a system for detecting a targetnucleic acid, the system comprising a reagent chamber and a supportmedium for detection of the first detectable signal. The reagent chambercomprises a guide nucleic acid targeting a target sequence; aprogrammable nuclease capable of being activated when complexed with theguide nucleic acid and the target sequence; and a single strandeddetector nucleic acid comprising a detection moiety, wherein thedetector nucleic acid is capable of being cleaved by the activatednuclease, thereby generating a first detectable signal.

Further described herein is a method of detecting a target nucleic acidin a sample comprising contacting the sample with a guide nucleic acidtargeting a target sequence, a programmable nuclease capable of beingactivated when complexed with the guide nucleic acid and the targetsequence, a single stranded detector nucleic acid comprising a detectionmoiety, wherein the detector nucleic acid is capable of being cleaved bythe activated nuclease, thereby generating a first detectable signal,and presenting the first detectable signal using a support medium. Themethod is applicable for use in the devices disclosed herein, forexample in a pneumatic valve device, a sliding valve device, a rotatingvalve device, or a lateral flow device.

Also described herein are various designs of assays for programmablenuclease diagnostics, such as CRISPR-Cas diagnostics. The design andformat of the lateral flow assays disclosed herein can includereporters, which can be tethered to the surface of a reaction chamberthat is upstream of the lateral flow strip itself. The assay designsdisclosed herein provide significant advantages as they minimize thechances of false positives, and thus can have improved sensitivity andspecificity for a target nucleic acid.

Also described herein is a kit for detecting a target nucleic acid. Thekit may comprise a support medium; a guide nucleic acid targeting atarget sequence; a programmable nuclease capable of being activated whencomplexed with the guide nucleic acid and the target sequence; and asingle stranded detector nucleic acid comprising a detection moiety,wherein the detector nucleic acid is capable of being cleaved by theactivated nuclease, thereby generating a first detectable signal.

The kits described herein may be used for detecting in a biologicalsample the presence or absence of a target nucleic acid. In someaspects, a biological sample from an individual or an environmentalsample can be tested to determine whether the individual has acommunicable disease. The biological sample can be tested to detect thepresence or absence of at least one target nucleic acid from a bacteriumor a virus or a pathogen responsible for the disease. The at least onetarget nucleic acid from a bacterium or a pathogen responsible for thedisease that is detected can also indicate that the bacterium orpathogen is wild-type or comprises a mutation that confers resistance totreatment, such as antibiotic treatment. The biological sample can betested to detect the presence or absence of at least one target nucleicacid expressed in a cancer or genetic disorder. A sample from anindividual or from an environment is applied to the reagents describedherein. The reaction between the sample and the reagents may beperformed in the reagent chamber provided in the kit or on a supportmedium provided in the kit. If the target nucleic acid is present in thesample, the target nucleic acid binds to the guide nucleic acid toactivate the programmable nuclease. The activated programmable nucleasecleaves the detector nucleic acid and generates a detectable signal thatcan be visualized on the support medium. If the target nucleic acid isabsent in the sample or below the threshold of detection, the guidenucleic acid remains unbound, the programmable nuclease remainsinactivated, and the detector nucleic acid remains uncleaved. After thesample and the reagents are contacted for a predetermined time, thereacted sample is placed on a sample pad of a support medium. The samplecan be placed on to the sample pad by dipping the support medium intothe reagent chamber, applying the reacted sample to the sample pad, orallowing the sample to transport if the reagent was initially placed onthe support medium. As the reacted sample and reagents move along thesupport medium to a detection region and after a predetermined amount oftime after applying the reacted sample, a positive control marker can bevisualized in the detection region. If the sample is positive for thetarget nucleic acid, a test marker for the detectable signal can also bevisualized. The results in the detection region can be visualized by eyeor using a mobile device. In some instances, an individual can open amobile application for reading of the test results on a mobile devicehaving a camera and take an image of the support medium, including thedetection region, barcode, reference color scale, and fiduciary markerson the housing, using the camera of the mobile device and the graphicuser interface (GUI) of the mobile application. The mobile applicationcan identify the test, visualize the detection region in the image, andanalyze to determine the presence or absence or the level of the targetnucleic acid responsible for the disease, cancer, or genetic disorder.The mobile application can present the results of the test to theindividual, store the test results in the mobile application, orcommunicate with a remote device and transfer the data of the testresults.

Such devices, systems, fluidic devices, kits, and methods describedherein may allow for detection of target nucleic acid, and in turn thepathogen and disease associated with the target nucleic acid or thecancer or genetic disorder associated with the target nucleic acid, inremote regions or low resource settings without specialized equipment.Also, such devices, systems, fluidic devices, kits, and methodsdescribed herein may allow for detection of target nucleic acid, and inturn the pathogen and disease associated with the target nucleic acid orthe cancer or genetic disorder associated with the target nucleic acid,in healthcare clinics or doctor offices without specialized equipment.In some cases, this provides a point of care testing for users to easilytest for a disease, cancer, or genetic disorder at home or quickly in anoffice of a healthcare provider. For example, a microfluidic device(e.g., a pneumatic valve device, a sliding valve device, or a rotatingvalve device) or a lateral flow device disclosed herein may be used incombination with reagents and methods disclosed herein to detect thepresence or absence of a target nucleic acid associated with a diseaseor pathogen in a biological sample rapidly and without specializedequipment. Assays that deliver results in under an hour, for example, infrom 15 to 60 minutes, are particularly desirable for at home testingfor many reasons. Antivirals can be most effective when administeredwithin the first 48 hours and improve antiviral stewardship. Thus, thesystems and assays disclosed herein, which are capable of deliveringresults in under an hour can will allow for the delivery of anti-viraltherapy at an optimal time. Additionally, the systems and assaysprovided herein, which are capable of delivering quick diagnoses andresults, can help keep or send a patient at home, improve comprehensivedisease surveillance, and prevent the spread of an infection. In othercases, this provides a test, which can be used in a lab to detect anucleic acid of interest in a sample from a subject. In particular,provided herein are devices, systems, fluidic devices, and kits, whereinthe rapid lab tests can be performed in a single system. In some cases,this may be valuable in detecting diseases and pathogens, cancer, or agenetic disorder in a developing country and as a global healthcare toolto detect the spread of a disease or efficacy of a treatment or provideearly detection of a cancer or genetic disorder.

To detect a target nucleic acid (e.g., a target nucleic acid associatedwith a disease), some methods as described herein use an editingtechnique, such as a technique using an editing enzyme or a programmablenuclease and guide nucleic acid. Methods comprising editing techniquesmay be used in combination with the microfluidic devices, lateral flowdevices, sample preparation devices, and compositions (e.g.,programmable nucleases, guide RNAs, reagents for in vitro transcription,amplification, reverse transcription, and reporters, or any combinationthereof) described herein. An editing enzyme or a programmable nucleasein the editing technique can be activated by a target nucleic acid,after which the activated editing enzyme or activated programmablenuclease can cleave nearby single-stranded nucleic acids, such detectornucleic acids with a detection moiety. A target nucleic acid from amarker, such as a disease or cancer marker, can be amplified byisothermal amplification and then an editing technique can be used todetect the marker. In some instances, the editing technique can comprisean editing enzyme or programmable nuclease that, when activated, cleavesnearby RNA or DNA as the readout of the detection. The methods asdescribed herein in some instances comprise obtaining a cell-free DNAsample, amplifying DNA from the sample, using an editing technique tocleave detector nucleic acids, and reading the output of the editingtechnique. In other instances, the method comprises obtaining a fluidsample from a patient, and without amplifying a nucleic acid of thefluid sample, using an editing technique to cleave detector nucleicacids, and detecting the nucleic acid. The method can also compriseusing single-stranded detector DNA, cleaving the single-strandeddetector DNA using an activated editing enzyme, wherein the editingenzyme cleaves at least 50% of a population of single-stranded detectorDNA as measured by a change in color. A number of samples, guide nucleicacids, programmable nucleases or editing enzymes, support mediums,target nucleic acids, single-stranded detector nucleic acids, andreagents are consistent with the devices, systems, fluidic devices,kits, and methods disclosed herein.

Also disclosed herein are detector nucleic acids (which can also bereferred to as reporters) and methods detecting a target nucleic usingthe detector nucleic acids. The detector nucleic acids disclosed hereinare applicable in the methods and devices (e.g., microfluidic devicesand lateral flow devices) disclosed herein. Often, the detector nucleicacid is a protein-nucleic acid, wherein the protein can allow fordetection of a signal (e.g., the protein is an enzyme and produces adetectable signal when contacting its substrate or the protein is asubstrate and produces a detectable signal when contacting its enzyme).For example, a method of assaying for a target nucleic acid in a samplecomprises contacting the sample to a complex comprising a guide nucleicacid comprising a segment that is reverse complementary to a segment orportion of the target nucleic acid and a programmable nuclease thatexhibits sequence independent cleavage upon forming a complex comprisingthe segment or portion of the guide nucleic acid binding to the segmentor portion of the target nucleic acid; and assaying for a signalindicating cleavage of at least some protein-nucleic acids of apopulation of protein-nucleic acids, wherein the signal indicates apresence of the target nucleic acid in the sample and wherein absence ofthe signal or a presence of the signal near background indicates anabsence of the target nucleic acid in the sample. Often, theprotein-nucleic acid is an enzyme-nucleic acid or an enzymesubstrate-nucleic acid. Sometimes, the protein-nucleic acid is attachedto a solid support. The nucleic acid can be DNA, RNA, or a DNA/RNAhybrid.

The methods described herein use a programmable nuclease, such as theCRISPR/Cas system, to detect a target nucleic acid. A method of assayingfor a target nucleic acid in a sample, for example, comprises: a)contacting the sample to a complex comprising a guide nucleic acidcomprising a segment that is reverse complementary to a segment of thetarget nucleic acid and a programmable nuclease that exhibits sequenceindependent cleavage upon forming a complex comprising the segment ofthe guide nucleic acid binding to the segment of the target nucleicacid; b) contacting the complex to a substrate; c) contacting thesubstrate to a reagent that differentially reacts with a cleavedsubstrate; and d) assaying for a signal indicating cleavage of thesubstrate, wherein the signal indicates a presence of the target nucleicacid in the sample and wherein absence of the signal or a presence ofthe signal near background indicates an absence of the target nucleicacid in the sample. Often, the substrate is an enzyme-nucleic acid.Sometimes, the substrate is an enzyme substrate-nucleic acid.

Cleavage of the protein-nucleic acid produces a signal. For example,cleavage of the protein-nucleic acid produces a calorimetric signal, apotentiometric signal, an amperometric signal, an optical signal, or apiezo-electric signal. Various devices can be used to detect thesedifferent types of signals, which indicate whether a target nucleic acidis present in the sample.

The present disclosure provides methods of assaying for a target nucleicacid as described herein. For example, a method of assaying for a targetnucleic acid in a sample comprises contacting the sample to a complexcomprising a guide nucleic acid comprising a segment that is reversecomplementary to a segment of the target nucleic acid and a programmablenuclease that exhibits sequence independent cleavage upon forming acomplex comprising the segment of the guide nucleic acid binding to thesegment of the target nucleic acid; and assaying for a signal indicatingcleavage of at least some protein-nucleic acids of a population ofprotein-nucleic acids, wherein the signal indicates a presence of thetarget nucleic acid in the sample and wherein absence of the signal or apresence of the signal near background indicates an absence of thetarget nucleic acid in the sample. As another example, a method ofassaying for a target nucleic acid in a sample, for example, comprises:a) contacting the sample to a complex comprising a guide nucleic acidcomprising a segment that is reverse complementary to a segment of thetarget nucleic acid and a programmable nuclease that exhibits sequenceindependent cleavage upon forming a complex comprising the segment ofthe guide nucleic acid binding to the segment of the target nucleicacid; b) contacting the complex to a substrate; c) contacting thesubstrate to a reagent that differentially reacts with a cleavedsubstrate; and d) assaying for a signal indicating cleavage of thesubstrate, wherein the signal indicates a presence of the target nucleicacid in the sample and wherein absence of the signal or a presence ofthe signal near background indicates an absence of the target nucleicacid in the sample. Often, the substrate is an enzyme-nucleic acid.Sometimes, the substrate is an enzyme substrate-nucleic acid. Themethods of assaying for a target nucleic acid in a sample disclosedherein are particularly suited for use in conjunction with the devicesand compositions disclosed herein.

Sample

A number of samples are consistent with the devices, systems, fluidicdevices, kits, and methods disclosed herein. These samples are, forexample, consistent with fluidic devices disclosed herein for detectionof a target nucleic acid within the sample, wherein the fluidic devicemay comprise multiple pumps, valves, reservoirs, and chambers for samplepreparation, amplification of a target nucleic acid within the sample,mixing with a programmable nuclease, and detection of a detectablesignal arising from cleavage of detector nucleic acids by theprogrammable nuclease within the fluidic system itself. These samplescan comprise a target nucleic acid for detection of an ailment, such asa disease, cancer, or genetic disorder, or genetic information, such asfor phenotyping, genotyping, or determining ancestry and are compatiblewith the reagents and support mediums as described herein. Generally, asample from an individual or an animal or an environmental sample can beobtained to test for presence of a disease, cancer, genetic disorder, orany mutation of interest. A biological sample from the individual may beblood, serum, plasma, saliva, urine, mucosal sample, peritoneal sample,cerebrospinal fluid, gastric secretions, nasal secretions, sputum,pharyngeal exudates, urethral or vaginal secretions, an exudate, aneffusion, or tissue. A tissue sample may be dissociated or liquifiedprior to application to detection system of the present disclosure. Asample from an environment may be from soil, air, or water. In someinstances, the environmental sample is taken as a swab from a surface ofinterest or taken directly from the surface of interest. In someinstances, the raw sample is applied to the detection system. In someinstances, the sample is diluted with a buffer or a fluid orconcentrated prior to application to the detection system or be appliedneat to the detection system. Sometimes, the sample is contained in nomore 20 μl. The sample, in some cases, is contained in no more than 1,5, 10, 15, 20, 25, 30, 35 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100,200, 300, 400, 500 μl, or any of value from 1 μl to 500 μl. In somecases, the sample is contained in from 1 μL to 500 μL, from 10 μL to 500μL, from 50 μL to 500 μL, from 100 μL to 500 μL, from 200 μL to 500 μL,from 300 μL to 500 μL, from 400 μL to 500 μL, from 1 μL to 200 μL, from10 μL to 200 μL, from 50 μL to 200 μL, from 100 μL to 200 μL, from 1 μLto 100 μL, from 10 μL to 100 μL, from 50 μL to 100 μL, from 1 μL to 50μL, from 10 μL to 50 μL, from 1 μL to 20 μL, from 10 μL to 20 μL, orfrom 1 μL to 10 μL. Sometimes, the sample is contained in more than 500μl.

In some instances, the sample is taken from single-cell eukaryoticorganisms; a plant or a plant cell; an algal cell; a fungal cell; ananimal cell, tissue, or organ; a cell, tissue, or organ from aninvertebrate animal; a cell, tissue, fluid, or organ from a vertebrateanimal such as fish, amphibian, reptile, bird, and mammal; a cell,tissue, fluid, or organ from a mammal such as a human, a non-humanprimate, an ungulate, a feline, a bovine, an ovine, and a caprine. Insome instances, the sample is taken from nematodes, protozoans,helminths, or malarial parasites. In some cases, the sample comprisesnucleic acids from a cell lysate from a eukaryotic cell, a mammaliancell, a human cell, a prokaryotic cell, or a plant cell. In some cases,the sample comprises nucleic acids expressed from a cell.

The sample used for disease testing may comprise at least one targetsequence that can bind to a guide nucleic acid of the reagents describedherein. In some cases, the target sequence is a portion of a nucleicacid. A nucleic acid can be from a genomic locus, a transcribed mRNA, ora reverse transcribed cDNA. A a nucleic acid can be from 5 to 100, 5 to90, 5 to 80, 5 to 70, 5 to 60, 5 to 50, 5 to 40, 5 to 30, 5 to 25, 5 to20, 5 to 15, or 5 to 10 nucleotides in length. A nucleic acid can befrom 10 to 90, from 20 to 80, from 30 to 70, or from 40 to 60nucleotides in length. A nucleic acid sequence can be from 10 to 95,from 20 to 95, from 30 to 95, from 40 to 95, from 50 to 95, from 60 to95, from 10 to 75, from 20 to 75, from 30 to 75, from 40 to 75, from 50to 75, from 5 to 50, from 15 to 50, from 25 to 50, from 35 to 50, orfrom 45 to 50 nucleotides in length. A nucleic acid can be 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 60, 70,80, 90, or 100 nucleotides in length. The target nucleic acid can bereverse complementary to a guide nucleic acid. In some cases, at least5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45,50, 60, 70, 80, 90, or 100 nucleotides of a guide nucleic acid can bereverse complementary to a target nucleic acid.

In some cases, the target sequence is a portion of a nucleic acid from avirus or a bacterium or other agents responsible for a disease in thesample. The target sequence, in some cases, is a portion of a nucleicacid from a sexually transmitted infection or a contagious disease, inthe sample. The target sequence, in some cases, is a portion of anucleic acid from an upper respiratory tract infection, a lowerrespiratory tract infection, or a contagious disease, in the sample. Thetarget sequence, in some cases, is a portion of a nucleic acid from ahospital acquired infection or a contagious disease, in the sample. Thetarget sequence, in some cases, is a portion of a nucleic acid fromsepsis, in the sample. These diseases may include but are not limited tohuman immunodeficiency virus (HIV), human papillomavirus (HPV),chlamydia, gonorrhea, syphilis, trichomoniasis, sexually transmittedinfection, malaria, Dengue fever, Ebola, chikungunya, and leishmaniasis.Pathogens include viruses, fungi, helminths, protozoa, malarialparasites, Plasmodium parasites, Toxoplasma parasites, and Schistosomaparasites. Helminths include roundworms, heartworms, and phytophagousnematodes, flukes, Acanthocephala, and tapeworms. Protozoan infectionsinclude infections from Giardia spp., Trichomonas spp., Africantrypanosomiasis, amoebic dysentery, babesiosis, balantidial dysentery,Chaga's disease, coccidiosis, malaria and toxoplasmosis. Examples ofpathogens such as parasitic/protozoan pathogens include, but are notlimited to: Plasmodium falciparum, P. vivax, Trypanosoma cruzi andToxoplasma gondii. Fungal pathogens include, but are not limited toCryptococcus neoformans, Histoplasma capsulatum, Coccidioides immitis,Blastomyces dermatitidis, Chlamydia trachomatis, and Candida albicans.Pathogenic viruses include but are not limited to immunodeficiency virus(e.g., HIV); influenza virus; dengue; West Nile virus; herpes virus;yellow fever virus; Hepatitis Virus C; Hepatitis Virus A; HepatitisVirus B; papillomavirus; and the like. Pathogens include, e.g., HIVvirus, Mycobacterium tuberculosis, Klebsiella pneumoniae, Acinetobacterbaumannii, Burkholderia cepacia, Streptococcus agalactiae,methicillin-resistant Staphylococcus aureus, Legionella pneumophila,Streptococcus pyogenes, Escherichia coli, Neisseria gonorrhoeae,Neisseria meningitidis, Pneumococcus, Cryptococcus neoformans,Histoplasma capsulatum, Hemophilus influenzae B, Treponema pallidum,Lyme disease spirochetes, Pseudomonas aeruginosa, Mycobacterium leprae,Brucella abortus, rabies virus, influenza virus, cytomegalovirus, herpessimplex virus I, herpes simplex virus II, human serum parvo-like virus,respiratory syncytial virus (RSV), M. genitalium, T. Vaginalis,varicella-zoster virus, hepatitis B virus, hepatitis C virus, measlesvirus, adenovirus, human T-cell leukemia viruses, Epstein-Barr virus,murine leukemia virus, mumps virus, vesicular stomatitis virus, Sindbisvirus, lymphocytic choriomeningitis virus, wart virus, blue tonguevirus, Sendai virus, feline leukemia virus, Reovirus, polio virus,simian virus 40, mouse mammary tumor virus, dengue virus, rubella virus,West Nile virus, Plasmodium falciparum, Plasmodium vivax, Toxoplasmagondii, Trypanosoma rangeli, Trypanosoma cruzi, Trypanosoma rhodesiense,Trypanosoma brucei, Schistosoma mansoni, Schistosoma japonicum, Babesiabovis, Eimeria tenella, Onchocerca volvulus, Leishmania tropica,Mycobacterium tuberculosis, Trichinella spiralis, Theileria parva,Taenia hydatigena, Taenia ovis, Taenia saginata, Echinococcusgranulosus, Mesocestoides corti, Mycoplasma arthritidis, M. hyorhinis,M. orale, M. arginini, Acholeplasma laidlawii, M. salivarium, M.pneumoniae, Enterobacter cloacae, Kiebsiella aerogenes, Proteusvulgaris, Serratia macesens, Enterococcus faecalis, Enterococcusfaecium, Streptococcus intermdius, Streptococcus pneumoniae, andStreptococcus pyogenes. Often the target nucleic acid comprises asequence from a virus or a bacterium or other agents responsible for adisease that can be found in the sample. In some cases, the targetnucleic acid is a portion of a nucleic acid from a genomic locus, atranscribed mRNA, or a reverse transcribed cDNA from a gene locus in atleast one of: human immunodeficiency virus (HIV), human papillomavirus(HPV), chlamydia, gonorrhea, syphilis, trichomoniasis, sexuallytransmitted infection, malaria, Dengue fever, Ebola, chikungunya, andleishmaniasis. Pathogens include viruses, fungi, helminths, protozoa,malarial parasites, Plasmodium parasites, Toxoplasma parasites, andSchistosoma parasites. Helminths include roundworms, heartworms, andphytophagous nematodes, flukes, Acanthocephala, and tapeworms. Protozoaninfections include infections from Giardia spp., Trichomonas spp.,African trypanosomiasis, amoebic dysentery, babesiosis, balantidialdysentery, Chaga's disease, coccidiosis, malaria and toxoplasmosis.Examples of pathogens such as parasitic/protozoan pathogens include, butare not limited to: Plasmodium falciparum, P. vivax, Trypanosoma cruziand Toxoplasma gondii. Fungal pathogens include, but are not limited toCryptococcus neoformans, Histoplasma capsulatum, Coccidioides immitis,Blastomyces dermatitidis, Chlamydia trachomatis, and Candida albicans.Pathogenic viruses include but are not limited to immunodeficiency virus(e.g., HIV); influenza virus; dengue; West Nile virus; herpes virus;yellow fever virus; Hepatitis Virus C; Hepatitis Virus A; HepatitisVirus B; papillomavirus; and the like. Pathogens include, e.g., HIVvirus, Mycobacterium tuberculosis, Streptococcus agalactiae,methicillin-resistant Staphylococcus aureus, Legionella pneumophila,Streptococcus pyogenes, Escherichia coli, Neisseria gonorrhoeae,Neisseria meningitidis, Pneumococcus, Cryptococcus neoformans,Histoplasma capsulatum, Hemophilus influenzae B, Treponema pallidum,Lyme disease spirochetes, Pseudomonas aeruginosa, Mycobacterium leprae,Brucella abortus, rabies virus, influenza virus, cytomegalovirus, herpessimplex virus I, herpes simplex virus II, human serum parvo-like virus,respiratory syncytial virus (RSV), M. genitalium, T. vaginalis,varicella-zoster virus, hepatitis B virus, hepatitis C virus, measlesvirus, adenovirus, human T-cell leukemia viruses, Epstein-Barr virus,murine leukemia virus, mumps virus, vesicular stomatitis virus, Sindbisvirus, lymphocytic choriomeningitis virus, wart virus, blue tonguevirus, Sendai virus, feline leukemia virus, Reovirus, polio virus,simian virus 40, mouse mammary tumor virus, dengue virus, rubella virus,West Nile virus, Plasmodium falciparum, Plasmodium vivax, Toxoplasmagondii, Trypanosoma rangeli, Trypanosoma cruzi, Trypanosoma rhodesiense,Trypanosoma brucei, Schistosoma mansoni, Schistosoma japonicum, Babesiabovis, Eimeria tenella, Onchocerca volvulus, Leishmania tropica,Mycobacterium tuberculosis, Trichinella spiralis, Theileria parva,Taenia hydatigena, Taenia ovis, Taenia saginata, Echinococcusgranulosus, Mesocestoides corti, Mycoplasma arthritidis, M. hyorhinis,M. orale, M. arginini, Acholeplasma laidlawii, M. salivarium and M.pneumoniae. In some cases, the target sequence is a portion of a nucleicacid from a genomic locus, a transcribed mRNA, or a reverse transcribedcDNA from a gene locus of bacterium or other agents responsible for adisease in the sample comprising a mutation that confers resistance to atreatment, such as a single nucleotide mutation that confers resistanceto antibiotic treatment.

The sample used for cancer testing may comprise at least one targetnucleic acid segment that can bind to a guide nucleic acid of thereagents described herein. The target nucleic acid segment, in somecases, is a portion of a nucleic acid from a gene with a mutationassociated with cancer, from a gene whose overexpression is associatedwith cancer, a tumor suppressor gene, an oncogene, a checkpointinhibitor gene, a gene associated with cellular growth, a geneassociated with cellular metabolism, or a gene associated with cellcycle. Sometimes, the target nucleic acid encodes for a cancerbiomarker, such as a prostate cancer biomarker or non-small cell lungcancer. In some cases, the assay can be used to detect “hotspots” intarget nucleic acids that can be predictive of lung cancer. In somecases, the target nucleic acid is a portion of a nucleic acid that isassociated with a blood fever. In some cases, the target nucleic acidsegment is a portion of a nucleic acid from a genomic locus, atranscribed mRNA, or a reverse transcribed cDNA from a locus of at leastone of: ALK, APC, ATM, AXIN2, BAP1, BARD1, BLM, BMPR1A, BRCA1, BRCA2,BRIP1, CASR, CDC73, CDH1, CDK4, CDKN1B, CDKN1C, CDKN2A, CEBPA, CHEK2,CTNNA1, DICERI, DIS3L2, EGFR, EPCAM, FH, FLCN, GATA2, GPC3, GREM1,HOXB13, HRAS, KIT, MAX, MEN1, MET, MITF, MLH1, MSH2, MSH3, MSH6, MUTYH,NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PMS2, POLD1, POLE, POT1,PRKAR1A, PTCH1, PTEN, RAD50, RAD51C, RAD51D, RB1, RECQL4, RET, RUNX1,SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, STK11,SUFU, TERC, TERT, TMEM127, TP53, TSC1, TSC2, VHL, WRN, and WT1.

The sample used for genetic disorder testing may comprise at least onetarget nucleic acid segment that can bind to a guide nucleic acid of thereagents described herein. In some embodiments, the genetic disorder ishemophilia, sickle cell anemia, 0-thalassemia, Duchene musculardystrophy, severe combined immunodeficiency, or cystic fibrosis. Thetarget nucleic acid segment, in some cases, is a portion of a nucleicacid from a gene with a mutation associated with a genetic disorder,from a gene whose overexpression is associated with a genetic disorder,from a gene associated with abnormal cellular growth resulting in agenetic disorder, or from a gene associated with abnormal cellularmetabolism resulting in a genetic disorder. In some cases, the targetnucleic acid segment is a portion of a nucleic acid from a genomiclocus, a transcribed mRNA, or a reverse transcribed cDNA from a locus ofat least one of: CFTR, FMR1, SMN1, ABCB11, ABCC8, ABCD1, ACAD9, ACADM,ACADVL, ACAT1, ACOX1, ACSF3, ADA, ADAMTS2, ADGRG1, AGA, AGL, AGPS, AGXT,AIRE, ALDH3A2, ALDOB, ALG6, ALMS1, ALPL, AMT, AQP2, ARG1, ARSA, ARSB,ASL, ASNS, ASPA, ASS1, ATM, ATP6V1B1, ATP7A, ATP7B, ATRX, BBS1, BBS10,BBS12, BBS2, BCKDHA, BCKDHB, BCS1L, BLM, BSND, CAPN3, CBS, CDH23,CEP290, CERKL, CHM, CHRNE, CIITA, CLN3, CLN5, CLN6, CLN8, CLRN1, CNGB3,COL27A1, COL4A3, COL4A4, COL4A5, COL7A1, CPS1, CPT1A, CPT2, CRB1, CTNS,CTSK, CYBA, CYBB, CYP11B1, CYP11B2, CYP17A1, CYP19A1, CYP27A1, DBT,DCLRElC, DHCR7, DHDDS, DLD, DMD, DNAH5, DNAI1, DNAI2, DYSF, EDA, EIF2B5,EMD, ERCC6, ERCC8, ESCO2, ETFA, ETFDH, ETHEl, EVC, EVC2, EYS, F9, FAH,FAM161A, FANCA, FANCC, FANCG, FH, FKRP, FKTN, G6 PC, GAA, GALC, GALK1,GALT, GAMT, GBA, GBE1, GCDH, GFM1, GJB1, GJB2, GLA, GLB1, GLDC, GLE1,GNE, GNPTAB, GNPTG, GNS, GRHPR, HADHA, HAX1, HBA1, HBA2, HBB, HEXA,HEXB, HGSNAT, HLCS, HMGCL, HOGA1, HPS1, HPS3, HSD17B4, HSD3B2, HYAL1,HYLS1, IDS, IDUA, IKBKAP, IL2 RG, IVD, KCNJ11, LAMA2, LAMA3, LAMB3,LAMC2, LCA5, LDLR, LDLRAP1, LHX3, LIFR, LIPA, LOXHD1, LPL, LRPPRC,MAN2B1, MCOLN1, MED17, MESP2, MFSD8, MKS1, MLC1, MMAA, MMAB, MMACHC,MMADHC, MPI, MPL, MPV17, MTHFR, MTM1, MTRR, MTTP, MUT, MYO7A, NAGLU,NAGS, NBN, NDRG1, NDUFAF5, NDUFS6, NEB, NPC1, NPC2, NPHS1, NPHS2, NR2E3,NTRK1, OAT, OPA3, OTC, PAH, PC, PCCA, PCCB, PCDH15, PDHA1, PDHB, PEX1,PEX10, PEX12, PEX2, PEX6, PEX7, PFKM, PHGDH, PKHD1, PMM2, POMGNT1, PPT1,PROP1, PRPS1, PSAP, PTS, PUS1, PYGM, RAB23, RAG2, RAPSN, RARS2, RDH12,RMRP, RPE65, RPGRIP1L, RS1, RTEL1, SACS, SAMHD1, SEPSECS, SGCA, SGCB,SGCG, SGSH, SLC12A3, SLC12A6, SLC17A5, SLC22A5, SLC25A13, SLC25A15,SLC26A2, SLC26A4, SLC35A3, SLC37A4, SLC39A4, SLC4A11, SLC6A8, SLC7A7,SMARCAL1, SMPD1, STAR, SUMF1, TAT, TCIRG1, TECPR2, TFR2, TGM1, TH,TMEM216, TPP1, TRMU, TSFM, TTPA, TYMP, USH1C, USH2A, VPS13A, VPS13B,VPS45, VRK1, VSX2, WNT10A, XPA, XPC, and ZFYVE26.

The sample used for phenotyping testing may comprise at least one targetnucleic acid segmentthat can bind to a guide nucleic acid of thereagents described herein. The target nucleic acid segment, in somecases, is a portion of a nucleic acid from a gene associated with aphenotypic trait.

The sample used for genotyping testing may comprise at least one targetnucleic acid segment that can bind to a guide nucleic acid of thereagents described herein. The target nucleic acid segment, in somecases, is a portion of a nucleic acid from a gene associated with agenotype.

The sample used for ancestral testing may comprise at least one targetnucleic acid segment that can bind to a guide nucleic acid of thereagents described herein. The target nucleic acid segment, in somecases, is a portion of a nucleic acid from a gene associated with ageographic region of origin or ethnic group.

The sample can be used for identifying a disease status. For example, asample is any sample described herein, and is obtained from a subjectfor use in identifying a disease status of a subject. The disease can bea cancer or genetic disorder. Sometimes, a method comprises obtaining aserum sample from a subject; and identifying a disease status of thesubject. Often, the disease status is prostate disease status.

In some instances, the target nucleic acid is a single stranded nucleicacid. Alternatively or in combination, the target nucleic acid is adouble stranded nucleic acid and is prepared into single strandednucleic acids before or upon contacting the reagents. The target nucleicacid may be a RNA, DNA, synthetic nucleic acids, or nucleic acids foundin biological or environmental samples. The target nucleic acids includebut are not limited to mRNA, rRNA, tRNA, non-coding RNA, long non-codingRNA, and microRNA (miRNA). In some cases, the target nucleic acid ismRNA. In some cases, the target nucleic acid is from a virus, aparasite, or a bacterium described herein. In some cases, the targetnucleic acid is transcribed from a gene as described herein.

A number of target nucleic acids are consistent with the methods andcompositions disclosed herein. Some methods described herein can detecta target nucleic acid present in the sample in various concentrations oramounts as a target nucleic acid population. In some cases, the samplehas at least 2 target nucleic acids. In some cases, the sample has atleast 3, 5, 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, 600, 700, 800,900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or 10000target nucleic acids. In some cases, the sample has from 1 to 10,000,from 100 to 8000, from 400 to 6000, from 500 to 5000, from 1000 to 4000,or from 2000 to 3000 target nucleic acids. In some cases, the sample hasfrom 100 to 9500, from 100 to 9000, from 100 to 8500, from 100 to 8000,from 100 to 7500, from 100 to 7000, from 100 to 6500, from 100 to 6000,from 100 to 5500, from 100 to 5000, from 250 to 9500, from 250 to 9000,from 250 to 8500, from 250 to 8000, from 250 to 7500, from 250 to 7000,from 250 to 6500, from 250 to 6000, from 250 to 5500, from 250 to 5000,from 2500 to 9500, from 2500 to 9000, from 2500 to 8500, from 2500 to8000, from 2500 to 7500, from 2500 to 7000, from 2500 to 6500, from 2500to 6000, from 2500 to 5500, or from 2500 to 5000 target nucleic acids.In some cases, the method detects target nucleic acid present at leastat one copy per 10¹ non-target nucleic acids, 10² non-target nucleicacids, 10′ non-target nucleic acids, 10⁴ non-target nucleic acids, 10⁵non-target nucleic acids, 10⁶ non-target nucleic acids, 107 non-targetnucleic acids, 10⁸ non-target nucleic acids, 10⁹ non-target nucleicacids, or 10¹⁰ non-target nucleic acids.

A number of target nucleic acid populations are consistent with themethods and compositions disclosed herein. Some methods described hereincan detect two or more target nucleic acid populations present in thesample in various concentrations or amounts. In some cases, the samplehas at least 2 target nucleic acid populations. In some cases, thesample has at least 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, or 50 targetnucleic acid populations. In some cases, the sample has from 3 to 50,from 5 to 40, or from 10 to 25 target nucleic acid populations. In somecases, the sample has from 2 to 50, from 5 to 50, from 10 to 50, from 2to 25, from 3 to 25, from 4 to 25, from 5 to 25, from 10 to 25, from 2to 20, from 3 to 20, from 4 to 20, from 5 to 20, from 10 to 20, from 2to 10, from 3 to 10, from 4 to 10, from 5 to 10, from 6 to 10, from 7 to10, from 8 to 10, or from 9 to 10 target nucleic acid populations. Insome cases, the method detects target nucleic acid populations that arepresent at least at one copy per 10¹ non-target nucleic acids, 102non-target nucleic acids, 103 non-target nucleic acids, 104 non-targetnucleic acids, 10⁵ non-target nucleic acids, 10⁶ non-target nucleicacids, 10⁷ non-target nucleic acids, 10′ non-target nucleic acids, 109non-target nucleic acids, or 10¹⁰ non-target nucleic acids. The targetnucleic acid populations can be present at different concentrations oramounts in the sample.

Additionally, a target nucleic acid can be amplified before binding to aguide nucleic acid, for example a crRNA of a CRISPR enzyme. Thisamplification can be PCR amplification or isothermal amplification. Thisnucleic acid amplification of the sample can improve at least one ofsensitivity, specificity, or accuracy of the detection the target RNA.The reagents for nucleic acid amplification can comprise a recombinase,a oligonucleotide primer, a single-stranded DNA binding (SSB) protein,and a polymerase. The nucleic acid amplification can be transcriptionmediated amplification (TMA). Nucleic acid amplification can be helicasedependent amplification (HDA) or circular helicase dependentamplification (cHDA). In additional cases, nucleic acid amplification isstrand displacement amplification (SDA). The nucleic acid amplificationcan be recombinase polymerase amplification (RPA). The nucleic acidamplification can be at least one of loop mediated amplification (LAMP)or the exponential amplification reaction (EXPAR). Nucleic acidamplification is, in some cases, by rolling circle amplification (RCA),ligase chain reaction (LCR), simple method amplifying RNA targets(SMART), single primer isothermal amplification (SPIA), multipledisplacement amplification (MDA), nucleic acid sequence basedamplification (NASBA), hinge-initiated primer-dependent amplification ofnucleic acids (HIP), nicking enzyme amplification reaction (NEAR), orimproved multiple displacement amplification (IMDA). The nucleic acidamplification can be performed for no greater than 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, or 60minutes. Sometimes, the nucleic acid amplification is performed for from1 to 60, from 5 to 55, from 10 to 50, from 15 to 45, from 20 to 40, orfrom 25 to 35 minutes. Sometimes, the nucleic acid amplification isperformed for from 5 to 60, from 10 to 60, from 15 to 60, from 30 to 60,from 45 to 60, from 1 to 45, from 5 to 45, from 10 to 45, from 30 to 45,from 1 to 30, from 5 to 30, from 10 to 30, from 15 to 30, from 1 to 15,from 5 to 15, or from 10 to 15 minutes. Sometimes, the nucleic acidamplification reaction is performed at a temperature of around 20-45° C.The nucleic acid amplification reaction can be performed at atemperature no greater than 20° C., 25° C., 30° C., 35° C., 37° C., 40°C., 45° C. The nucleic acid amplification reaction can be performed at atemperature of at least 20° C., 25° C., 30° C., 35° C., 37° C., 40° C.,or 45° C. In some cases, the nucleic acid amplification reaction isperformed at a temperature of from 20° C. to 45° C., from 25° C. to 40°C., from 30° C. to 40° C., or from 35° C. to 40° C. In some cases, thenucleic acid amplification reaction is performed at a temperature offrom 20° C. to 45° C., from 25° C. to 45° C., from 30° C. to 45° C.,from 35° C. to 45° C., from 40° C. to 45° C., from 20° C. to 37° C.,from 25° C. to 37° C., from 30° C. to 37° C., from 35° C. to 37° C.,from 20° C. to 30° C., from 25° C. to 30° C., from 20° C. to 25° C., orfrom 22° C. to 25° C.

Any of the above disclosed samples are consistent with the systems,assays, and programmable nucleases disclosed herein and can be used as acompanion diagnostic with any of the diseases disclosed herein (e.g.,RSV, sepsis, flu), or can be used in reagent kits, point-of-carediagnostics, or over-the-counter diagnostics.

Reagents

A number of reagents are consistent with the devices, systems, fluidicdevices, kits, and methods disclosed herein. These reagents are, forexample, consistent for use within various fluidic devices disclosedherein for detection of a target nucleic acid within the sample, whereinthe fluidic device may comprise multiple pumps, valves, reservoirs, andchambers for sample preparation, amplification of a target nucleic acidwithin the sample, mixing with a programmable nuclease, and detection ofa detectable signal arising from cleavage of detector nucleic acids bythe programmable nuclease within the fluidic system itself. Thesereagents are compatible with the samples, fluidic devices, methods ofdetection, and support mediums as described herein for detection of anailment, such as a disease, cancer, or genetic disorder, or geneticinformation, such as for phenotyping, genotyping, or determiningancestry. The reagents described herein for detecting a disease, cancer,or genetic disorder comprise a guide nucleic acid targeting the targetnucleic acid segment indicative of a disease, cancer, or geneticdisorder. Reagents of this disclosure can include guide nucleic acids,substrate nucleic acids, detection reagents, signal reagents, buffers,and programmable nucleases.

Guide Nucleic Acids

Guide nucleic acids are compatible for use in the devices describedherein (e.g., pneumatic valve devices, sliding valve devices, rotatingvalve devices, and lateral flow devices) and may be used in conjunctionwith compositions disclosed herein (e.g., programmable nucleases,reagents for in vitro transcription, reagents for amplification,reagents for reverse transcription, and reporters, or any combinationthereof) to carry out highly efficient, rapid, and accurate reactionsfor detecting whether a target nucleic acid is present in a sample(e.g., DETECTR reactions). The guide nucleic acid binds to the singlestranded target nucleic acid comprising a portion of a nucleic acid froma virus or a bacterium or other agents responsible for a disease asdescribed herein. The guide nucleic acid can bind to the single strandedtarget nucleic acid comprising a portion of a nucleic acid from abacterium or other agents responsible for a disease as described hereinand further comprising a mutation, such as a single nucleotidepolymorphism (SNP), which can confer resistance to a treatment, such asantibiotic treatment. The guide nucleic acid binds to the singlestranded target nucleic acid comprising a portion of a nucleic acid froma cancer gene or gene associated with a genetic disorder as describedherein. The guide nucleic acid is complementary to the target nucleicacid. Often the guide nucleic acid binds specifically to the targetnucleic acid. The target nucleic acid may be a RNA, DNA, or syntheticnucleic acids. A guide nucleic acid can comprise a sequence that isreverse complementary to the sequence of a target nucleic acid. A guidenucleic acid can be a crRNA. Sometimes, a guide nucleic acid comprises acrRNA and tracrRNA. The guide nucleic acid can bind specifically to thetarget nucleic acid. In some cases, the guide nucleic acid is notnaturally occurring and made by artificial combination of otherwiseseparate segments of sequence. Often, the artificial combination isperformed by chemical synthesis, by genetic engineering techniques, orby the artificial manipulation of isolated segments of nucleic acids.The target nucleic acid can be designed and made to provide desiredfunctions. In some cases, the targeting region of a guide nucleic acidis 20 nucleotides in length. The targeting region of the guide nucleicacid may have a length of at least 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length.In some instances, the targeting region of the guide nucleic acid is 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, or 30 nucleotides in length. In some cases, the targeting region ofa guide nucleic acid has a length from exactly or about 12 nucleotides(nt) to about 80 nt, from about 12 nt to about 50 nt, from about 12 ntto about 45 nt, from about 12 nt to about 40 nt, from about 12 nt toabout 35 nt, from about 12 nt to about 30 nt, from about 12 nt to about25 nt, from about 12 nt to about 20 nt, from about 12 nt to about 19 nt,from about 19 nt to about 20 nt, from about 19 nt to about 25 nt, fromabout 19 nt to about 30 nt, from about 19 nt to about 35 nt, from about19 nt to about 40 nt, from about 19 nt to about 45 nt, from about 19 ntto about 50 nt, from about 19 nt to about 60 nt, from about 20 nt toabout 25 nt, from about 20 nt to about 30 nt, from about 20 nt to about35 nt, from about 20 nt to about 40 nt, from about 20 nt to about 45 nt,from about 20 nt to about 50 nt, or from about 20 nt to about 60 nt. Insome cases, the targeting region of a guide nucleic acid has a length offrom about 10 nt to about 60 nt, from about 20 nt to about 50 nt, orfrom about 30 nt to about 40 nt. In some cases, the targeting region ofa guide nucleic acid has a length of from 15 nt to 55 nt, from 25 nt to55 nt, from 35 nt to 55 nt, from 45 nt to 55 nt, from 15 nt to 45 nt,from 25 nt to 45 nt, from 35 nt to 45 nt, from 15 nt to 35 nt, from 25nt to 35 nt, or from 15 nt to 25 nt. It is understood that the sequenceof a polynucleotide need not be 100% complementary to that of its targetnucleic acid to be specifically hybridizable or hybridizable or bindspecifically. The guide nucleic acid can have a sequence comprising atleast one uracil in a region from nucleic acid residue 5 to 20 that isreverse complementary to a modification variable region in the targetnucleic acid. The guide nucleic acid, in some cases, has a sequencecomprising at least one uracil in a region from nucleic acid residue 5to 9, 10 to 14, or 15 to 20 that is reverse complementary to amodification variable region in the target nucleic acid. The guidenucleic acid can have a sequence comprising at least one uracil in aregion from nucleic acid residue 5 to 20 that is reverse complementaryto a methylation variable region in the target nucleic acid. The guidenucleic acid, in some cases, has a sequence comprising at least oneuracil in a region from nucleic acid residue 5 to 9, 10 to 14, or 15 to20 that is reverse complementary to a methylation variable region in thetarget nucleic acid.

The guide nucleic acid can be selected from a group of guide nucleicacids that have been tiled against the nucleic acid of a strain of aninfection or genomic locus of interest. The guide nucleic acid can beselected from a group of guide nucleic acids that have been tiledagainst the nucleic acid of a strain of HPV 16 or HPV18. Often, guidenucleic acids that are tiled against the nucleic acid of a strain of aninfection or genomic locus of interest can be pooled for use in a methoddescribed herein. Often, these guide nucleic acids are pooled fordetecting a target nucleic acid in a single assay. The pooling of guidenucleic acids that are tiled against a single target nucleic acid canenhance the detection of the target nucleic using the methods describedherein. The pooling of guide nucleic acids that are tiled against asingle target nucleic acid can ensure broad coverage of the targetnucleic acid within a single reaction using the methods describedherein. The tiling, for example, is sequential along the target nucleicacid. Sometimes, the tiling is overlapping along the target nucleicacid. In some instances, the tiling comprises gaps between the tiledguide nucleic acids along the target nucleic acid. In some instances thetiling of the guide nucleic acids is non-sequential. Often, a method fordetecting a target nucleic acid comprises contacting a target nucleicacid to a pool of guide nucleic acids and a programmable nuclease,wherein a guide nucleic acid of the pool of guide nucleic acids has asequence selected from a group of tiled guide nucleic acid that isreverse complementary to a sequence of a target nucleic acid; andassaying for a signal produce by cleavage of at least some detectornucleic acids of a population of detector nucleic acids. Pooling ofguide nucleic acids can ensure broad spectrum identification, or broadcoverage, of a target species within a single reaction. This can beparticularly helpful in diseases or indications, like sepsis, that maybe caused by multiple organisms.

Programmable Nucleases

Programmable nucleases described herein are compatible for use in thedevices described herein (e.g., pneumatic valve devices, sliding valvedevices, rotating valve devices, and lateral flow devices) and may beused in conjunction with compositions disclosed herein (e.g., guidenucleic acids, reagents for in vitro transcription, reagents foramplification, reagents for reverse transcription, reporters, or anycombination thereof) to carry out highly efficient, rapid, and accuratereactions for detecting whether a target nucleic acid is present in asample (e.g., DETECTR reactions). A programmable nuclease can comprise aprogrammable nuclease capable of being activated when complexed with aguide nucleic acid and target nucleic acid. The programmable nucleasecan become activated after binding of a guide nucleic acid with a targetnucleic acid, in which the activated programmable nuclease can cleavethe target nucleic acid and can have trans cleavage activity. Transcleavage activity can be non-specific cleavage of nearby single-strandednucleic acids by the activated programmable nuclease, such as transcleavage of detector nucleic acids with a detection moiety. Once thedetector nucleic acid is cleaved by the activated programmable nuclease,the detection moiety can be released from the detector nucleic acid andcan generate a signal. A signal can be a calorimetric, potentiometric,amperometric, optical (e.g., fluorescent, colorometric, etc.), orpiezo-electric signal. Often, the signal is present prior to detectornucleic acid cleavage and changes upon detector nucleic acid cleavage.Sometimes, the signal is absent prior to detector nucleic acid cleavageand is present upon detector nucleic acid cleavage. The detectablesignal can be immobilized on a support medium for detection. Theprogrammable nuclease can be a CRISPR-Cas (clustered regularlyinterspaced short palindromic repeats—CRISPR associated) nucleoproteincomplex with trans cleavage activity, which can be activated by bindingof a guide nucleic acid with a target nucleic acid. The CRISPR-Casnucleoprotein complex can comprise a Cas protein (also referred to as aCas nuclease) complexed with a guide nucleic acid, which can also bereferred to as CRISPR enzyme. A guide nucleic acid can be a CRISPR RNA(crRNA). Sometimes, a guide nucleic acid comprises a crRNA and atrans-activating crRNA (tracrRNA).

The CRISPR/Cas system used to detect a modified target nucleic acids cancomprise CRISPR RNAs (crRNAs), trans-activating crRNAs (tracrRNAs), Casproteins, and detector nucleic acids.

Described herein are reagents comprising a programmable nuclease capableof being activated when complexed with the guide nucleic acid and thetarget nucleic acid segment or portion. A programmable nuclease can becapable of being activated when complexed with a guide nucleic acid andthe target sequence. The programmable nuclease can be activated uponbinding of the guide nucleic acid to its target nucleic acid anddegrades non-specifically nucleic acid in its environment. Theprogrammable nuclease has trans cleavage activity once activated. Aprogrammable nuclease can be a Cas protein (also referred to,interchangeably, as a Cas nuclease). A crRNA and Cas protein can form aCRISPR enzyme.

Several programmable nucleases are consistent with the methods anddevices of the present disclosure. For example, CRISPR/Cas enzymes areprogrammable nucleases used in the methods and systems disclosed herein.CRISPR/Cas enzymes can include any of the known Classes and Types ofCRISPR/Cas enzymes. Programmable nucleases disclosed herein includeClass 1 CRISPR/Cas enzymes, such as the Type I, Type IV, or Type IIICRISPR/Cas enzymes. Programmable nucleases disclosed herein also includethe Class 2 CRISPR/Cas enzymes, such as the Type II, Type V, and Type VICRISPR/Cas enzymes. Preferable programmable nucleases included in theseveral devices disclosed herein (e.g., a microfluidic device such as apneumatic valve device or a sliding valve device or a lateral flowassay) and methods of use thereof include a Type V or Type VI CRISPR/Casenzyme.

In some embodiments, the Type V CRISPR/Cas enzyme is a programmableCas12 nuclease. Type V CRISPR/Cas enzymes (e.g., Cas12 or Cas14) lack anHNH domain. A Cas12 nuclease of the present disclosure cleaves a nucleicacids via a single catalytic RuvC domain. The RuvC domain is within anuclease, or “NUC” lobe of the protein, and the Cas12 nucleases furthercomprise a recognition, or “REC” lobe. The REC and NUC lobes areconnected by a bridge helix and the Cas12 proteins additionally includetwo domains for PAM recognition termed the PAM interacting (PK) domainand the wedge (WED) domain. (Murugan et al., Mol Cell. 2017 Oct. 5;68(1): 15-25). A programmable Cas12 nuclease can be a Cas12a (alsoreferred to as Cpf1) protein, a Cas12b protein, Cas12c protein, Cas12dprotein, or a Cas12e protein. In some cases, a suitable Cas12 proteincomprises an amino acid sequence having at least 80%, at least 850%, atleast 90%, at least 950%, at least 98%, at least 99%, or 100%, aminoacid sequence identity to any one of SEQ ID NO: 145—SEQ ID NO: 155.

TABLE 1  Cas12 Protein Sequences SEQ ID NO Description Sequence 145Lachnospiraceae MSKLEKFTNCYSLSKTLRFKAIPVGKTQENIDNKRLLVEDEKRAEDYKGVbacterium KKLLDRYYLSFINDVLHSIKLKNLNNYISLFRKKTRTEKENKELENLEINLR ND2006KEIAKAFKGNEGYKSLFKKDIIETILPEFLDDKDEIALVNSFNGFTTAFTGF (LbCas12a)FDNRENMFSEEAKSTSIAFRCINENLTRYISNMDIFEKVDAIFDKHEVQEIK EKILNSDYDVEDFFEGEFFNFVLTQEGIDVYNAIIGGFVTESGEKIKGLNEYINLYNQKTKQKLPKFKPLYKQVLSDRESLSFYGEGYTSDEEVLEVFRNTLNKNSEIFSSIKKLEKLFKNFDEYSSAGIFVKNGPAISTISKDIFGEWNVIRDK WNAEYDDIHLKKKAVVTEKYEDDRRKSFKKIGSFSLEQLQEYADADLSVVEKLKEIIIQKVDEIYKVYGSSEKLFDADFVLEKSLKKNDAVVAIMKDLLDSVKSFENYIKAFFGEGKETNRDESFYGDFVLAYDILLKVDHIYDAIRNYVTQKPYSKDKFKLYFQNPQFMGGWDKDKETDYRATILRYGSKYYLAIMDK KYAKCLQKIDKDDVNGNYEKINYKLLPGPNKMLPKVFFSKKWMAYYNPSEDIQKIYKNGTFKKGDMFNLNDCHKLIDFFKDSISRYPKWSNAYDFNFSETEKYKDIAGFYREVEEQGYKVSFESASKKEVDKLVEEGKLYMFQIYNKDFSDKSHGTPNLHTMYFKLLFDENNHGQIRLSGGAELFMRRASLKKEELVVHPANSPIANKNPDNPKKTTTLSYDVYKDKRFSEDQYELHIPIAINKCPKNIFKINTEVRVLLKHDDNPYVIGIDRGERNLLYIVVVDGKGNIVEQYSLNEIINNFNGIRIKTDYHSLLDKKEKERFEARQNWTSIENIKELKAGYISQVVHKICELVEKYDAVIALEDLNSGFKNSRVKVEKQVYQKFEKMLIDKLNYMVDK KSNPCATGGALKGYQITNKFESFKSMSTQNGFIFYIPAWLTSKIDPSTGFVNLLKTKYTSIADSKKFISSFDRIMYVPEEDLFEFALDYKNFSRTDADYIKK WKLYSYGNRIRIFRNPKKNNVFDWEEVCLTSAYKELFNKYGINYQGDIRALLCEQSDKAFYSSFMALMSLMLQMRNSITGRTDVDFLISPVKNSDGIFYDSRNYEAQENAILPKNADANGAYNIARKVLWAIGQFKKAEDEKLDKVKI AISNKEWLEYAQTSVKH 146Acidaminococcus  MTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKELK sp. BV316 PIIDRIYKTYADQCLQLVQLDWENLSAAIDSYRKEKTEETRNALIEEQATY (AsCas12a)RNAIHDYFIGRTDNLTDAINKRHAEIYKGLFKAELFNGKVLKQLGTVTTTEHENALLRSFDKFTTYFSGFYENRKNVFSAEDISTAIPHRIVQDNFPKFKENCHIFTRLITAVPSLREHFENVKKAIGIFVSTSIEEVFSFPFYNQLLTQTQIDLYNQLLGGISREAGTEKIKGLNEVLNLAIQKNDETAHIIASLPHRFIPLFKQILSDRNTLSFILEEFKSDEEVIQSFCKYKTLLRNENVLETAEALFNELNSIDLTHIFISHKKLETISSALCDHWDTLRNALYERRISELTGKITKSAKEKVQRSLKHEDINLQEIISAAGKELSEAFKQKTSEILSHAHAALDQPLPTTLKKQEEKEILK SQLDSLLGLYHLLDWFAVDESNEVDPEFSARLTGIKLEMEPSLSFYNKARNYATKKPYSVEKFKLNFQMPTLASGWDVNKEKNNGAILFVKNGLYYLGIMPKQKGRYKALSFEPTEKTSEGFDKMYYDYFPDAAKMIPKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITKEIYDLNNPEKEPKKFQTAYAKKTGDQKGYREALCKWIDFTRDFLSKYTKTTSIDLSSLRPSSQYKDLGEYYAELNPLLYHISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHEIGKPNLHTLYWTGLFSPENLAKTSIKLNGQAELFYRPKSRMKRMAHRLGEKMLNKKLKDQKTPIPDTLYQELYDYVNHRLSHDLSDEARALLPNVITKEVSHEIIKDRRFTSDKFFFHVPITLNYQAANSPSKFNQRVNAYLKEHPETPIIGIDRGERNLIYITVIDS TGKILEQRSLNTIQQFDYQKKLDNREKERVAARQAWSVVGTIKDLKQGYLSQVIHEIVDLMIHYQAVVVLENLNFGFKSKRTGIAEKAVYQQFEKMLIDKLNCLVLKDYPAEKVGGVLNPYQLTDQFTSFAKMGTQSGFLFYVPAPYTSKIDPLTGFVDPFVWKTIKNHESRKHFLEGFDFLHYDVKTGDFILHFKMNRNLSFQRGLPGFMPAWDIVFEKNETQFDAKGTPFIAGKRIVPVIENHRFTGRYRDLYPANELIALLEEKGIVFRDGSNILPKLLENDDSHAIDTMVALIRSVLQMRNSNAATGEDYINSPVRDLNGVCFDSRFQNPEWPMDADANGAYHIALKGQLLLNHLKESKDLKLQNGISNQDWLAYIQELRN 147 FrancisellaMSIYQEFVNKYSLSKTLRFELIPQGKTLENIKARGLILDDEKRAKDYKKAK  novicidaQIIDKYHQFFIEEILSSVCISEDLLQNYSDVYFKLKKSDDDNLQKDFKSAKD U112TIKKQISEYIKDSEKFKNLFNQNLIDAKKGQESDLILWLKQSKDNGIELFKA (FnCas12a)NSDITDIDEALEIIKSFKGWTTYFKGFHENRKNVYSSNDIPTSIIYRIVDDNLPKFLENKAKYESLKDKAPEAINYEQIKKDLAEELTFDIDYKTSEVNQRVFS LDEVFEIANFNNYLNQSGITKFNTIIGGKFVNGENTKRKGINEYINLYSQQINDKTLKKYKMSVLFKQILSDTESKSFVIDKLEDDSDVVTTMQSFYEQIAAFKTVEEKSIKETLSLLFDDLKAQKLDLSKIYFKNDKSLTDLSQQVFDDYSVIGTAVLEYITQQIAPKNLDNPSKKEQELIAKKTEKAKYLSLETIKLALEEFNKHRDIDKQCRFEEILANFAAIPMIFDEIAQNKDNLAQISIKYQNQGKKDLLQASAEDDVKAIKDLLDQTNNLLHKLKIFHISQSEDKANILDKDEHFYLVFEECYFELANIVPLYNKIRNYITQKPYSDEKFKLNFENSTLANGWDKNKEPDNTAILFIKDDKYYLGVMNKKNNKIFDDKAIKENKGEGYKKIVYKLLPGANKMLPKVFFSAKSIKFYNPSEDILRIRNHSTHTKNGSPQKGYEKFEFNIEDCRKFIDFYKQSISKHPEWKDFGFRFSDTQRYNSIDEFYREVENQGYKLTFENIS ESYIDSVVNQGKLYLFQIYNKDFSAYSKGRPNLHTLYWKALFDERNLQDVVYKLNGEAELFYRKQSIPKKITHPAKEAIANKNKDNPKKESVFEYDLIK DKRFTEDKFFFHCPITINFKSSGANKFNDEINLLLKEKANDVHILSIDRGERHLAYYTLVDGKGNIIKQDTFNIIGNDRMKTNYHDKLAAIEKDRDSARKDWKKINNIKEMKEGYLSQVVHEIAKLVIEYNAIVVFEDLNFGFKRGRFKVEKQVYQKLEKMLIEKLNYLVFKDNEFDKTGGVLRAYQLTAPFETFKKMGK QTGIIYYVPAGFTSKICPVTGFVNQLYPKYESVSKSQEFFSKFDKICYNLDK GYFEFSFDYKNFGDKAAKGKWTIASFGSRLINFRNSDKNHNWDTREVYPTKELEKLLKDYSIEYGHGECIKAAICGESDKKFFAKLTSVLNTILQMRNSK TGTELDYLISPVADVNGNFFDSRQAPKNMPQDADANGAYHIGLKGLMLLGRIKNNQEGKKLNLVIKNEEYFEFVQNRNN 148 Porphyromonas MKTQHFFEDFTSLYSLSKTIRFELKPIGKTLENIKKNGLIRRDEQRLDDYEK  macacaeLKKVIDEYHEDFIANILSSFSFSEEILQSYIQNLSESEARAKIEKTMRDTLAK  (PmCas12a)AFSEDERYKSIFKKELVKKDIPVWCPAYKSLCKKFDNFTTSLVPFHENRK NLYTSNEITASIPYRIVHVNLPKFIQNIEALCELQKKMGADLYLEMMENLRNVWPSFVKTPDDLCNLKTYNHLMVQSSISEYNRFVGGYSTEDGTKHQGINEWINIYRQRNKEMRLPGLVFLHKQILAKVDSSSFISDTLENDDQVFCVLRQFRKLFWNTVSSKEDDAASLKDLFCGLSGYDPEAIYVSDAHLATISKNIFDRWNYISDAIRRKTEVLMPRKKESVERYAEKISKQIKKRQSYSLAELDDLLAHYSEESLPAGFSLLSYFTSLGGQKYLVSDGEVILYEEGSNIWDEVLIAFRDLQVILDKDFTEKKLGKDEEAVSVIKKALDSALRLRKFFDLLSGTGAEIRRDSSFYALYTDRMDKLKGLLKMYDKVRNYLTKKPYSIEKFKLHFDNPSLLSGWDKNKELNNLSVIFRQNGYYYLGIMTPKGKNLFKTLPKLGAEEMFYEKMEYKQIAEPMLMLPKVFFPKKTKPAFAPDQSVVDIYNKKTFKTGQKGFNKKDLYRLIDFYKEALTVHEWKLFNFSFSPTEQYRNIGEFFDEVREQAYK VSMVNVPASYIDEAVENGKLYLFQIYNKDFSPYSKGIPNLHTLYWKALFS EQNQSRVYKLCGGGELFYRKASLHMQDTTVHPKGISIHKKNLNKKGETS LFNYDLVKDKRFTEDKFFFHVPISINYKNKKITNVNQMVRDYIAQNDDLQIIGIDRGERNLLYISRIDTRGNLLEQFSLNVIESDKGDLRTDYQKILGDREQERLRRRQEWKSIESIKDLKDGYMSQVVHKICNMVVEHKAIVVLENLNLSFMKGRKKVEKSVYEKFERMLVDKLNYLVVDKKNLSNEPGGLYAAYQLTNPLFSFEELHRYPQSGILFFVDPWNTSLTDPSTGFVNLLGRINYTNVGDARK FFDRFNAIRYDGKGNILFDLDLSRFDVRVETQRKLWTLTTFGSRIAKSKKS GKWMVERIENLSLCFLELFEQFNIGYRVEKDLKKAILSQDRKEFYVRLIYLFNLMMQIRNSDGEEDYILSPALNEKNLQFDSRLIEAKDLPVDADANGAYNVARKGLMVVQRIKRGDHESIHRIGRAQWLRYVQEGIVE 149 Moraxella MLFQDFTHLYPLSKTVRFELKPIDRTLEHIHAKNFLSQDETMADMHQKVK  bovoculiVILDDYHRDFIADMMGEVKLTKLAEFYDVYLKFRKNPKDDELQKQLKDL 237QAVLRKEIVKPIGNGGKYKAGYDRLFGAKLFKDGKELGDLAKFVIAQEG (MbCas12a)ESSPKLAHLAHFEKFSTYFTGFHDNRKNMYSDEDKHTAIAYRLIHENLPRFIDNLQILTTIKQKHSALYDQIINELTASGLDVSLASHLDGYHKLLTQEGITAYNTLLGGISGEAGSPKIQGINELINSFIHNQHCHKSERIAKLRPLHKQILSDGMSVSFLPSKFADDSEMCQAVNEFYRHYADVFAKVQSLFDGFDDHQKDGIYVEHKNLNELSKQAFGDFALLGRVLDGYYVDVVNPEFNERFAKAKTDNAKAKLTKEKDKFIKGVHSLASLEQAIEHYTARHDDESVQAGKLGQYFKHGLAGVDNPIQKIHNNHSTIKGFLERERPAGERALPKIKSGKNPEMTQLRQLKELLDNALNVAHFAKLLTTKTTLDNQDGNFYGEFGVLYDELAKIPTLYNKVRDYLSQKPFSTEKYKLNFGNPTLLNGWDLNKEKDNFGVILQKDGCYYLALLDKAHKKVFDNAPNTGKSIYQKMIYKYLEVRKQFPKVFFSKEAIAINYHPSKELVEIKDKGRQRSDDERLKLYRFILECLKIHPKYDKKFEGAIGDIQLFKKDKKGREVPISEKDLFDKINGIFSSKPKLEMEDFFIGEFKRYNPSQDLVDQYNIYKKIDSNDNRKKENFYNNHPKFKKDLVRYYYESMCKHEEWEESFEFSKKLQDIGCYVDVNELFTEIETRRLNYKISFCNINADYIDELVEQGQLYLFQIYNKDFSPKAHGKPNLHTLYFKALFSEDNLADPIYKLNGEAQIFYRKAS LDMNETTIHRAGEVLENKNPDNPKKRQFVYDIIKDKRYTQDKFMLHVPITMNFGVQGMTIKEFNKKVNQSIQQYDEVNVIGIDRGERHLLYLTVINSKGEILEQCSLNDITTASANGTQMTTPYHKILDKREIERLNARVGWGEIETIKELK SGYLSHVVHQISQLMLKYNAIVVLEDLNFGFKRGRFKVEKQIYQNFENALIKKLNHLVLKDKADDEIGSYKNALQLTNNFTDLKSIGKQTGFLFYVPAWNTSKIDPETGFVDLLKPRYENIAQSQAFFGKFDKICYNADKDYFEFHIDYAK FTDKAKNSRQIWTICSHGDKRYVYDKTANQNKGAAKGINVNDELKSLFARHHINEKQPNLVMDICQNNDKEFHKSLMYLLKTLLALRYSNASSDEDFILSPVANDEGVFFNSALADDTQPQNADANGAYHIALKGLWLLNELKNSDDL NKVKLAIDNQTWLNFAQNR150 Moraxella MGIHGVPAALFQDFTHLYPLSKTVRFELKPIGRTLEHIHAKNFLSQDETMAbovoculi DMYQKVKVILDDYHRDFIADMMGEVKLTKLAEFYDVYLKFRKNPKDDG AAX08_00205LQKQLKDLQAVLRKESVKPIGSGGKYKTGYDRLFGAKLFKDGKELGDLA (Mb2Cas12a)KFVIAQEGESSPKLAHLAHFEKFSTYFTGFHDNRKNMYSDEDKHTAIAYRLIHENLPRFIDNLQILTTIKQKHSALYDQIINELTASGLDVSLASHLDGYHK LLTQEGITAYNRIIGEVNGYTNKHNQICHKSERIAKLRPLHKQILSDGMGVSFLPSKFADDSEMCQAVNEFYRHYTDVFAKVQSLFDGFDDHQKDGIYVEHKNLNELSKQAFGDFALLGRVLDGYYVDVVNPEFNERFAKAKTDNAKAKLTKEKDKFIKGVHSLASLEQAIEHHTARHDDESVQAGKLGQYFKHGLAGVDNPIQKIHNNHSTIKGFLERERPAGERALPKIKSGKNPEMTQLRQLKELLDNALNVAHFAKLLTTKTTLDNQDGNFYGEFGVLYDELAKIPTLYNKVRDYLSQKPFSTEKYKLNFGNPTLLNGWDLNKEKDNFGVILQKDGCYYLALLDKAHKKVFDNAPNTGKNVYQKMVYKLLPGPNKMLPKVFFAKSNLDYYNPSAELLDKYAKGTHKKGDNFNLKDCHALIDFFKAGINKHPEWQHFGFK FSPTSSYRDLSDFYREVEPQGYQVKFVDINADYIDELVEQGKLYLFQIYNK DFSPKAHGKPNLHTLYFKALFSEDNLADPIYKLNGEAQIFYRKASLDMNETTIHRAGEVLENKNPDNPKKRQFVYDIIKDKRYTQDKFMLHVPITMNFGVQGMTIKEFNKKVNQSIQQYDEVNVIGIDRGERHLLYLTVINSKGEILEQRS LNDITTASANGTQVTTPYHKILDKREIERLNARVGWGEIETIKELKSGYLS HVVHQINQLMLKYNAIVVLEDLNFGFKRGRFKVEKQIYQNFENALIKKLNHLVLKDKADDEIGSYKNALQLTNNFTDLKSIGKQTGFLFYVPAWNTSKIDPETGFVDLLKPRYENIAQSQAFFGKFDKICYNTDKGYFEFHIDYAKFTDKAKNSRQKWAICSHGDKRYVYDKTANQNKGAAKGINVNDELKSLFARYHINDKQPNLVMDICQNNDKEFHKSLMCLLKTLLALRYSNASSDEDFILSPVANDEGVFFNSALADDTQPQNADANGAYHIALKGLWLLNELKNSDDLNKV KLAIDNQTWLNFAQNR 151Moraxella MGIHGVPAALFQDFTHLYPLSKTVRFELKPIGKTLEHIHAKNFLNQDETM bovoculiADMYQKVKAILDDYHRDFIADMMGEVKLTKLAEFYDVYLKFRKNPKDD AAX11_00205GLQKQLKDLQAVLRKEIVKPIGNGGKYKAGYDRLFGAKLFKDGKELGDL (Mb3Cas12a)AKFVIAQEGESSPKLAHLAHFEKFSTYFTGFHDNRKNMYSDEDKHTAIAYRLIHENLPRFIDNLQILATIKQKHSALYDQIINELTASGLDVSLASHLDGYHKLLTQEGITAYNTLLGGISGEAGSRKIQGINELINSFIHNQHCHKSERIAKLRPLHKQILSDGMGVSFLPSKFADDSEVCQAVNEFYRHYADVFAKVQSLFDGFDDYQKDGIYVEYKNLNELSKQAFGDFALLGRVLDGYYVDVVNPEFNERFAKAKTDNAKAKLTKEKDKFIKGVHSLASLEQAIEHYTARHDDESVQAGKLGQYFKHGLAGVDNPIQKIHNNHSTIKGFLERERPAGERALPKIKSDKS PEIRQLKELLDNALNVAHFAKLLTTKTTLHNQDGNFYGEFGALYDELAKIATLYNKVRDYLSQKPFSTEKYKLNFGNPTLLNGWDLNKEKDNFGVILQK DGCYYLALLDKAHKKVFDNAPNTGKSVYQKMIYKLLPGPNKMLPKVFFAKSNLDYYNPSAELLDKYAQGTHKKGDNFNLKDCHALIDFFKAGINKHPEWQHFGFKFSPTSSYQDLSDFYREVEPQGYQVKFVDINADYINELVEQGQLYLFQIYNKDFSPKAHGKPNLHTLYFKALFSEDNLVNPIYKLNGEAEIFYRKASLDMNETTIHRAGEVLENKNPDNPKKRQFVYDIIKDKRYTQDKFMLHVPITMNFGVQGMTIKEFNKKVNQSIQQYDEVNVIGIDRGERHLLYLTVINS KGEILEQRSLNDITTASANGTQMTTPYHKILDKREIERLNARVGWGEIETIKELKSGYLSHVVHQISQLMLKYNAIVVLEDLNFGFKRGRFKVEKQIYQNFENALIKKLNHLVLKDKADDEIGSYKNALQLTNNFTDLKSIGKQTGFLFYVPAWNTSKIDPETGFVDLLKPRYENIAQSQAFFGKFDKICYNADRGYFEFHIDYAKFNDKAKNSRQIWKICSHGDKRYVYDKTANQNKGATIGVNVNDELKSLFTRYHINDKQPNLVMDICQNNDKEFHKSLMYLLKTLLALRYSNASSDEDFILSPVANDEGVFFNSALADDTQPQNADANGAYHIALKGLWLLNELK NSDDLNKVKLAIDNQTWLNFAQNR 152 ThiomicrospiraMGIHGVPAATKTFDSEFFNLYSLQKTVRFELKPVGETASFVEDFKNEGLK  sp. XS5RVVSEDERRAVDYQKVKEIIDDYHRDFIEESLNYFPEQVSKDALEQAFHL (TsCas12a)YQKLKAAKVEEREKALKEWEALQKKLREKVVKCFSDSNKARFSRIDKKELIKEDLINWLVAQNREDDIPTVETFNNFTTYFTGFHENRKNIYSKDDHATAISFRLIHENLPKFFDNVISFNKLKEGFPELKFDKVKEDLEVDYDLKHAFEIEYFVNFVTQAGIDQYNYLLGGKTLEDGTKKQGMNEQINLFKQQQTRDKARQIPKLIPLFKQILSERTESQSFIPKQFESDQELFDSLQKLHNNCQDKFTVLQQAILGLAEADLKKVFIKTSDLNALSNTIFGNYSVFSDALNLYKESLKTKKAQEAFEKLPAHSIHDLIQYLEQFNSSLDAEKQQSTDTVLNYFIKTDELYSRFIK STSEAFTQVQPLFELEALSSKRRPPESEDEGAKGQEGFEQIKRIKAYLDTLMEAVHFAKPLYLVKGRKMIEGLDKDQSFYEAFEMAYQELESLIIPIYNKARSYLSRKPFKADKFKINFDNNTLLSGWDANKETANASILFKKDGLYYLGIMPKGKTFLFDYFVSSEDSEKLKQRRQKTAEEALAQDGESYFEKIRYKLLPGASKMLPKVFFSNKNIGFYNPSDDILRIRNTASHTKNGTPQKGHSKVEFNLNDCHKMIDFFKSSIQKHPEWGSFGFTFSDTSDFEDMSAFYREVENQGYVIS FDKIKETYIQSQVEQGNLYLFQIYNKDFSPYSKGKPNLHTLYWKALFEEANLNNVVAKLNGEAEIFFRRHSIKASDKVVHPANQAIDNKNPHTEKTQSTFEYDLVKDKRYTQDKFFFHVPISLNFKAQGVSKFNDKVNGFLKGNPDVNIIGIDRGERHLLYFTVVNQKGEILVQESLNTLMSDKGHVNDYQQKLDKKEQERDAARKSWTTVENIKELKEGYLSHVVHKLAHLIIKYNAIVCLEDLNFGFKRGRFKVEKQVYQKFEKALIDKLNYLVFKEKELGEVGHYLTAYQLTAPFESFKKLGKQSGILFYVPADYTSKIDPTTGFVNFLDLRYQSVEKAKQLLSDFNAIRFNSVQNYFEFEIDYKKLTPKRKVGTQSKWVICTYGDVRYQNRRNQKGHWETEEVNVTEKLKALFASDSKTTTVIDYANDDNLIDVILEQDKASFFKELLWLLKLTMTLRHSKIKSEDDFILSPVKNEQGEFYDSRKAGEVWPKDADANGAYHIALKGLWNLQQINQWEKGKTLNLAIKNQDWFSFIQEKPYQE 153 ButyrivibrioMGIHGVPAAYYQNLTKKYPVSKTIRNELIPIGKTLENIRKNNILESDVKRK  sp. NC3005QDYEHVKGIMDEYHKQLINEALDNYMLPSLNQAAEIYLKKHVDVEDREE (BsCas12a)FKKTQDLLRREVTGRLKEHENYTKIGKKDILDLLEKLPSISEEDYNALESFRNFYTYFTSYNKVRENLYSDEEKSSTVAYRLINENLPKFLDNIKSYAFVKAAGVLADCIEEEEQDALFMVETFNMTLTQEGIDMYNYQIGKVNSAINLYNQKNHKVEEFKKIPKMKVLYKQILSDREEVFIGEFKDDETLLSSIGAYGNVLMTYLKSEKINIFFDALRESEGKNVYVKNDLSKTTMSNIVFGSWSAFDELLNQEYDLANENKKKDDKYFEKRQKELKKNKSYTLEQMSNLSKEDISPIENYIERISEDIEKICIYNGEFEKIVVNEHDSSRKLSKNIKAVKVIKDYLDSIKELEHDIKLINGSGQELEKNLVVYVGQEEALEQLRPVDSLYNLTRNYLTKKPFSTEKVKLNFNKSTLLNGWDKNKETDNLGILFFKDGKYYLGIMNTTANKAFVNPPAAKTENVFKKVDYKLLPGSNKMLPKVFFAKSNIGYYNPSTELYSNYKKGTHKKGPSFSIDDCHNLIDFFKESIKKHEDWSKFGFEFSDTADYRDIS EFYREVEKQGYKLTFTDIDESYINDLIEKNELYLFQIYNKDFSEYSKGKLNLHTLYFMMLFDQRNLDNVVYKLNGEAEVFYRPASIAENELVIHKAGEGIK NKNPNRAKVKETSTFSYDIVKDKRYSKYKFTLHIPITMNFGVDEVRRFNDVINNALRTDDNVNVIGIDRGERNLLYVVVINSEGKILEQISLNSIINKEYDIETNYHALLDEREDDRNKARKDWNTIENIKELKTGYLSQVVNVVAKLVLKYNAIICLEDLNFGFKRGRQKVEKQVYQKFEKMLIEKLNYLVIDKSREQVSPEKMGGALNALQLTSKFKSFAELGKQSGIIYYVPAYLTSKIDPTTGFVNLFYIKYENIEKAKQFFDGFDFIRFNKKDDMFEFSFDYKSFTQKACGIRSKWIVYTNGERIIKYPNPEKNNLFDEKVINVTDEIKGLFKQYRIPYENGEDIKEIIISKAEADFYKRLFRLLHQTLQMRNSTSDGTRDYIISPVKNDRGEFFCSEFSEGTMPKDADANGAYNIARKGLWVLEQIRQKDEGEKVNLSMTNAEWLKYAQLH LL 154 AacCas12bMAVKSIKVKLRLDDMPEIRAGLWKLHKEVNAGVRYYTEWLSLLRQENLYRRSPNGDGEQECDKTAEECKAELLERLRARQVENGHRGPAGSDDELLQLARQLYELLVPQAIGAKGDAQQIARKFLSPLADKDAVGGLGIAKAGNKPRWVRMREAGEPGWEEEKEKAETRKSADRTADVLRALADFGLKPLMRVYTDSEMSSVEWKPLRKGQAVRTWDRDMFQQAIERMMSWESWNQRVGQEYAKLVEQKNRFEQKNFVGQEHLVHLVNQLQQDMKEASPGLESKEQTAHYVTGRALRGSDKVFEKWGKLAPDAPFDLYDAEIKNVQRRNTRRFGSHDLFAKLAEPEYQALWREDASFLTRYAVYNSILRKLNHAKMFATFTLPDATAHPIWTRFDKLGGNLHQYTFLFNEFGERRHAIRFHKLLKVENGVAREVDDVTVPISMSEQLDNLLPRDPNEPIALYFRDYGAEQHFTGEFGGAKIQCRRDQLAHMHRRRGARDVYLNVSVRVQSQSEARGERRPPYAAVFRLVGDNHRAFVHFDKLSDYLAEHPDDGKLGSEGLLSGLRVMSVDLGLRTSASISVFRVARKDELKPNSKGRVPFFFPIKGNDNLVAVHERSQLLKLPGETESKDLRAIREERQRTLRQLRTQLAYLRLLVRCGSEDVGRRERSWAKLIEQPVDAANHMTPDWREAFENELQKLKSLHGICSDKEWMDAVYESVRRVWRHMGKQVRDWRKDVRSGERPKIRGYAKDVVGGNSIEQIEYLERQYKFLKSWSFFGKVSGQVIRAEKGSRFAITLREHIDHAKEDRLKKLADRIIMEALGYVYALDERGK GKWVAKYPPCQLILLEELSEYQFNNDRPPSENNQLMQWSHRGVFQELINQAQVHDLLVGTMYAAFSSRFDARTGAPGIRCRRVPARCTQEHNPEPFPWWLNKFVVEHTLDACPLRADDLIPTGEGEIFVSPFSAEEGDFHQIHADLNAAQNLQQRLWSDFDISQIRLRCDWGEVDGELVLIPRLTGKRTADSYSNKVFYTNTGVTYYERERGKKRRKVFAQEKLSEEEAELLVEADEAREKSVVLMRDPSGIINRGNWTRQKEFWSMVNQRIEGYLVKQIRSRVPLQDSACENTGDI 155 VariantMKKIDNFVGCYPVSKTLRFKAIPIGKTQENIEKKRLVEEDEVRAKDYKAVKKLIDRYHREFIEGVLDNVKLDGLEEYYMLFNKSDREESDNKKIEEVIEERFRRVISKSFKNNEEYKKIFSKKIIEEILPNYIKDEEEKELVKGFKGFYTAFVGYAQNRENMYSDEKKSTAISYRIVNENIVIPRFITNIKVFEKAKSILDVDKINEINEYILNNDYYVDDFFNIDFFNYVLNQKGIDIYNAIIGGIVTGDGRKIQGLNECINLYNQENKKIRLPQFKPLYKQILSESESMSFYIDEIESDDMLIDMLKESLQIDSTINNAIDDLKVLFNNIFDYDLSGIFINNGLPITTISNDVYGQWSTISDGWNERYDVLSNAKDKES EKYFEKRRKEYKKVKSFSISDLQELGGKDLSICKKINEIISEMIDDYK SKIEEIQYLFDIKELEKPLVTDLNKIELIKNSLDGLKRIERYVIPFLGTGKEQNRDEVFYGYFIKCIDAIKEIDGVYNKTRNYLTKKPYSKDKFK LYFENPQLMGGWDRNKESDYRSTLLRKNGKYYVAIIDKSSSNCMMNIEEDENDNYEKINYKLLPGPNKMLPKVFFSKKNREYFAPSKEIERIYSTGTFKKDTNFVKKDCENLITFYKDSLDRHEDWSKSFDFSFKESS AYRDISEFYRDVEKQGYRVSFDLLSSNAVNTLVEEGKLYLFQLYNK DFSEKSHGIPNLHTMYFRSLFDDNNKGNIRLNGGAEMFMRRASLNKQDVTVHKANQPIKNKNLLNPKKTTTLPYDVYKDKRFTEDQYEVHIPITMNKVPNNPYKINHMVREQLVKDDNPYVIGIDRGERNLIYVVVVDGQGHIVEQLSLNEIINENNGISIRTDYHTLLDAKERERDESRKQWKQIENIKELKEGYISQVVHKICELVEKYDAVIALEDLNSGFKNSRVK VEKQVYQKFEKMLITKLNYMVDKKKDYNKPGGVLNGYQLTTQFESFSKMGTQNGIMFYIPAWLTSKMDPTTGFVDLLKPKYKNKADAQK FFSQFDSIRYDNQEDAFVFKVNYTKFPRTDADYNKEWEIYTNGERIRVFRNPKKNNEYDYETVNVSERMKELFDSYDLLYDKGELKETICEMEESKFFEELIKLFRLTLQMRNSISGRTDVDYLISPVKNSNGYFYNS NDYKKEGAKYPKDADANGAYNIARKVLWAIEQFKMADEDKLDK  TKISIKNQEWLEYAQTHCE

Alternatively, the Type V CRISPR/Cas enzyme is a programmable Cas14nuclease. A Cas14 protein of the present disclosure includes 3 partialRuvC domains (RuvC-I, RuvC-II, and RuvC-III, also referred to herein assubdomains) that are not contiguous with respect to the primary aminoacid sequence of the Cas14 protein, but form a RuvC domain once theprotein is produced and folds. A naturally occurring Cas14 proteinfunctions as an endonuclease that catalyzes cleavage at a specificsequence in a target nucleic acid. A programmable Cas14 nuclease can bea Cas14a protein, a Cas14b protein, a Cas14c protein, a Cas14d protein,a Cas14e protein, a Cas14f protein, a Cas14g protein, a Cas14h protein,or a Cas14u protein. In some cases, a suitable Cas14 protein comprisesan amino acid sequence having at least 80%, at least 85%, at least 90%,at least 95%, at least 98%, at least 99%, or 100%, amino acid sequenceidentity to any one of SEQ ID NO: 53—SEQ ID NO: 144.

TABLE 2—Cas14 Protein Sequences

TABLE 2 Cas14 Protein Sequences SEQ ID NO Sequence 53MEVQKTVMKTLSLRILRPLYSQEIEKEIKEEKERRKQAGGTGELDGGFYKKLEKKHSEMFSFDRLNLLLNQLQREIAKVYNHAISELYIATIAQGNKSNKHYISSIVYNRAYGYFYNAYIALGICSKVEANFRSNELLTQQSALPTAKSDNFPIVLHKQKGAEGEDGGFRISTEGSDLIFEIPIPFYEYNGENRKEPYKWVKKGGQKPVLKLILSTFRRQRNKGWAKDEGTDAEIRKVTEGKYQVSQIEINRGKKLGEHQKWFANFSIEQPIYERKPNRSIVGGLDVGIRSPLVCAINNSFSRYSVDSNDVFKFSKQVFAFRRRLLSKNSLKRKGHGAAHKLEPITEMTEKNDKFRKKIIERWAKEVTNFFVKNQVGIVQIEDLSTMKDREDHFFNQYLRGFWPYYQMQTLIENKLKEYGIEVKRVQAKYTSQLCSNPNCRYWNNYFNFEYRKVNKFPKFKCEKCNLEISADYNAARNLSTPDIEKFVAKATKGINLPEK  54MEEAKTVSKTLSLRILRPLYSAEIEKEIKEEKERRKQGGKSGELDSGFYKKLEKKHTQMFGWDKLNLMLSQLQRQIARVFNQSISELYIETVIQGKKSNKHYTSKIVYNRAYSVFYNAYLALGITSKVEANFRSTELLMQKSSLPTAKSDNFPILLHKQKGVEGEEGGFKISADGNDLIFEIPIPFYEYDSANKKEPFKWIKKGGQKPTIKLILSTFRRQRNKGWAKDEGTDAEIRKVIEGK YQVSHIEINRGKKLGDHQKWFVNFTIEQPIYERKLDKNIIGGIDVGIKSPLVCAVNNSFARYSVDSNDVLKFSKQAFAFRRRLLSKNSLKRSGHGSKNKLDPITRMTEKNDRFRKKIIERWAKEVTNFFIKNQVGTVQIEDLSTMKDRQDNFFNQYLRGFWPYYQMQNLIENKLKEYGIETKRIKARYTSQLCSNPSCRHWNSYFSFDHRKTNNFPKFKCEKCALEISADYNAARNISTPDIEKFVAKATKGINLPDKNENVILE 55MAKNTITKTLKLRIVRPYNSAEVEKIVADEKNNREKIALEKNKDKVKEACSKHLKVAAYCTTQVERNACLFCKARKLDDKFYQKLRGQFPDAVFWQEISEIFRQLQKQAAEIYNQSLIELYYEIFIKGKGIANASSVEHYLSDVCYTRAAELFKNAAIASGLRSKIKSNFRLKELKNMKS GLPTTKSDNFPIPLVKQKGGQYTGFEISNHNSDFIIKIPFGRWQVKKEIDKYRPWEKFDFEQVQKSPKPISLLLSTQRRKRNKGWSKDEGTEAEIKKVMNGDYQTSYIEVKRGSKIGEKS AWMLNLSIDVPKIDKGVDPSIIGGIDVGVKSPLVCAINNAFSRYSISDNDLFHFNKKMFARRRILLKKNRHKRAGHGAKNKLKPITILTEKSERFRKKLIERWACEIADFFIKNKVGTVQMENLESMKRKEDSYFNIRLRGFWPYAEMQNKIEFKLKQYGIEIRKVAPNNTSKTCSKCGHLNNYFNFEYRKKNKFPHFKCEKCNFKENADYNAALNISNPKLKSTKEEP 56MERQKVPQIRKIVRVVPLRILRPKYSDVIENALKKFKEKGDDTNTNDFWRAIRDRDTEFFRKELNFSEDEINQLERDTLFRVGLDNRVLFSYFDFLQEKLMKDYNKIISKLFINRQSKSSFENDLTDEEVEELIEKDVTPFYGAYIGKGIKSVIKSNLGGKFIKSVKIDRETKKVTKLTAINIGLMGLPVAKSDTFPIKIIKTNPDYITFQKSTKENLQKIEDYETGIEYGDLLVQITIPWFKNENKDFSLIKTKEAIEYYKLNGVGKKDLLNINLVLTTYHIRKKKSWQIDGSSQSLVREMANGELEEKWKSFFDTFIKKYGDEGKSALVKRRVNKKSRAKGEKGRELNLDERIKRLYDSIK AKSFPSEINLIPENYKWKLHFSIEIPPMVNDIDSNLYGGIDFGEQNIATLCVKNIEKDDYDFLTIYGNDLLKHAQASYARRRIMRVQDEYKARGHGKSRKTKAQEDYSERMQKLRQKITERLVKQISDFFLWRNKFHMAVCSLRYEDLNTLYKGESVKAKRMRQFINKQQLFNGIERKLKDYNSEIYVNSRYPHYTSRLCSKCGKLNLYFDFLKFRTKNIIIRKNPDGSEIKYMPFFICEFCGWKQAGDKNASANIADKDYQDKLNKEKEFCNIRKPKSKKEDIGEENEEERDYSRRFNRNSFIYNSLKKDNKLNQEKLFDEWKNQLKRKIDGRNKFEPKEYKDRFSYLFAYYQEIIKN ESES  57MVPTELITKTLQLRVIRPLYFEEIEKELAELKEQKEKEFEETNSLLLESKKIDAKSLKKLKRKARSSAAVEFWKIAKEKYPDILTKPEMEFIFSEMQKMMARFYNKSMTNIFIEMNNDEKVNPLSLISKASTEANQVIKCSSISSGLNRKIAGSINKTKFKQVRDGLISLPTARTETFPISFYKSTANKDEIPISKINLPSEEEADLTITLPFPFFEIKKEKKGQKAYSYFNIIEKSGRSNNKIDLLLSTHRRQRRKGWKEEGGTSAEIRRLMEGEFDKEWEIYLGEAEKSEKAKNDLIKNMTRGKLSKDIKEQLEDIQVKYFSDNNVESWNDLSKEQKQELSKLRKKKVEELKDWKHVKEILKTRAKIGWVELKRGKRQRDRNKWFVNITITRPPFINKELDDTKFGGIDLGVKVPFVCAVHGSPARLIIKENEILQFNKMVSARNRQITKDSEQRKGRGKKNKFIKKEIFNERNELFRKKIIERWANQIVKFFEDQKCATVQIENLESFDRTSYK  58MKSDTKDKKIIIHQTKTLSLRIVKPQSIPMEEFTDLVRYHQMIIFPVYNNGAIDLYKKLFK AKIQKGNEARAIKYFMNKIVYAPIANTVKNSYIALGYSTKMQSSFSGKRLWDLRFGEATPPTIKADFPLPFYNQSGFKVSSENGEFIIGIPFGQYTKKTVSDIEKKTSFAWDKFTLEDTTK KTLIELLLSTKTRKMNEGWKNNEGTEAEIKRVMDGTYQVTSLEILQRDDSWFVNFNIAYDSLKKQPDRDKIAGIHMGITRPLTAVIYNNKYRALSIYPNTVMHLTQKQLARIKEQRTNS KYATGGHGRNAKVTGTDTLSEAYRQRRKKIIEDWIASIVKFAINNEIGTIYLEDISNTNSFFAAREQKLIYLEDISNTNSFLSTYKYPISAISDTLQHKLEEKAIQVIRKKAYYVNQICSLCGHYNKGFTYQFRRKNKFPKMKCQGCLEATSTEFNAAANVANPDYEKLLIKHGLLQLKK  59MSTITRQVRLSPTPEQSRLLMAHCQQYISTVNVLVAAFDSEVLTGKVSTKDFRAALPSAVKNQALRDAQSVFKRSVELGCLPVLKKPHCQWNNQNWRVEGDQLILPICKDGKTQQERFRCAAVALEGKAGILRIKKKRGKWIADLTVTQEDAPESSGSAIMGVDLGIKVPAVAHIGGKGTRFFGNGRSQRSMRRRFYARRKTLQKAKKLRAVRKSKGKEARWMKTINHQLSRQIVNHAHALGVGTIKIEALQGIRKGTTRKSRGAAARKNNRMTNTWSFSQLTLFITYKAQRQGITVEQVDPAYTSQDCPACRARNGAQDRTYVCSECGWRGHRDTVGAINISRRAGLSGHRR GATGA 60MIAQKTIKIKLNPTKEQIIKLNSIIEEYIKVSNFTAKKIAEIQESFTDSGLTQGTCSECGKEKTYRKYHLLKKDNKLFCITCYKRKYSQFTLQKVEFQNKTGLRNVAKLPKTYYTNAIRFASDTFSGFDEIIKKKQNRLNSIQNRLNFWKELLYNPSNRNEIKIKVVKYAPKTDTREHPHYYSEAEIKGRIKRLEKQLKKFKMPKYPEFTSETISLQRELYSWKNPDELKISSITDKNESMNYYGKEYLKRYIDLINSQTPQILLEKENNSFYLCFPITKNIEMPKIDDTFEPVGIDWGITRNIAVVSILDSKTKKPKFVKFYSAGYILGKRKHYKSLRKHFGQKKRQDKINKLGTKEDRFIDSNIHK LAFLIVKEIRNHSNKPIILMENITDNREEAEKSMRQNILLHSVKSRLQNYIAYKALWNNIPTNLVKPEHTSQICNRCGHQDRENRPKGSKLFKCVKCNYMSNADFNASINIARKFYIGEYEPFYKDNEKMKSGVNSISM 61LKLSEQENITTGVKFKLKLDKETSEGLNDYFDEYGKAINFAIKVIQKELAEDRFAGKVRLDENKKPLLNEDGKKIWDFPNEFCSCGKQVNRYVNGKSLCQECYKNKFTEYGIRKRMYS AKGRKAEQDINIKNSTNKISKTHFNYAIREAFILDKSIKKQRKERFRRLREMKKKLQEFIEIRDGNKILCPKIEKQRVERYIHPSWINKEKKLEDFRGYSMSNVLGKIKILDRNIKREEKSLK EKGQINFKARRLMLDKSVKFLNDNKISFTISKNLPKEYELDLPEKEKRLNWLKEKIKIIKNQKPKYAYLLRKDDNFYLQYTLETEFNLKEDYSGIVGIDRGVSHIAVYTFVHNNGKNERPLFLNSSEILRLKNLQKERDRFLRRKHNKKRKKSNMRNIEKKIQLILHNYSKQIVDFAKNK NAFIVFEKLEKPKKNRSKMSKKSQYKLSQFTFKKLSDLVDYKAKREGIKVLYISPEYTSK ECSHCGEKVNTQRPFNGNSSLFKCNKCGVELNADYNASINIAKKGLNILNSTN 62MEESIITGVKFKLRIDKETTKKLNEYFDEYGKAINFAVKIIQKELADDRFAGKAKLDQNKNPILDENGKKIYEFPDEFCSCGKQVNKYVNNKPFCQECYKIRFTENGIRKRMYSAKGRKAEHKINILNSTNKISKTHFNYAIREAFILDKSIKKQRKKRNERLRESKKRLQQFIDMRDGKREICPTIKGQKVDRFIHPSWITKDKKLEDFRGYTLSIINSKIKILDRNIKREEKSLKEKGQIIFKAKRLMLDKSIRFVGDRKVLFTISKTLPKEYELDLPSKEKRLNWLKEKIEIIKNQKPKYAYLLRKNIESEKKPNYEYYLQYTLEIKPELKDFYDGAIGIDRGINHIAVCTFISNDGKVTPPKFFSSGEILRLKNLQKERDRFLLRKHNKNRKKGNMRVIENKINLILHRYSKQIVDMAKKLNASIVFEELGRIGKSRTKMKKSQRYKLSLFIFKKLSDLVDYKSRREGIRVTYVPPEYTSKECSHCGEKVNTQRPFNGNYSLFKCNKCGIQLNSDYNASINIAKKGLKIPNST 63LWTIVIGDFIEMPKQDLVTTGIKFKLDVDKETRKKLDDYFDEYGKAINFAVKIIQKNLKEDRFAGKIALGEDKKPLLDKDGKKIYNYPNESCSCGNQVRRYVNAKPFCVDCYKLKFTENGIRKRMYSARGRKADSDINIKNSTNKISKTHFNYAIREGFILDKSLKKQRSKRIKKLLELKRKLQEFIDIRQGQMVLCPKIKNQRVDKFIHPSWLKRDKKLEEFRGYSLSVVEGKIKIFNRNILREEDSLRQRGHVNFKANRIMLDKSVRFLDGGKVNFNLNKGLPKEYLLDLPKKENK LSWLNEKISLIKLQKPKYAYLLRREGSFFIQYTIENVPKTFSDYLGAIGIDRGISHIAVCTFVSKNGVNKAPVFFSSGEILKLKSLQKQRDLFLRGKHNKIRKKSNMRNIDNKINLILHKYSRNIVNLAKSEKAFIVFEKLEKIKKSRFKMSKSLQYKLSQFTFKKLSDLVEYKAKIEGIKVDYVPPEYTSKECSHCGEKVDTQRPFNGNSSLFKCNKCRVQLNADYNASINIAKKSLNISN 64MSKTTISVKLKIIDLSSEKKEFLDNYFNEYAKATTFCQLRIRRLLRNTHWLGKKEKSSKK WIFESGICDLCGENKELVNEDRNSGEPAKICKRCYNGRYGNQMIRKLFVSTKKREVQENMDIRRVAKLNNTHYHRIPEEAFDMIKAADTAEKRRKKNVEYDKKRQMEFIEMFNDEKK RAARPKKPNERETRYVHISKLESPSKGYTLNGIKRKIDGMGKKIERAEKGLSRKKIFGYQGNRIKLDSNWVRFDLAESEITIPSLFKEMKLRITGPTNVHSKSGQIYFAEWFERINKQPNNYCYLIRKTSSNGKYEYYLQYTYEAEVEANKEYAGCLGVDIGCSKLAAAVYYDSKNKKAQKPIEIFTNPIKKIKMRREKLIKLLSRVKVRHRRRKLMQLSKTEPIIDYTCHKTARKIVEMANTAKAFISMENLETGIKQKQQARETKKQKFYRNMFLFRKLSKLIEYKALLKGIKIVYVK PDYTSQTCSSCGADKEKTERPSQAIFRCLNPTCRYYQRDINADFNAAVNIAKKALNNTEV VTTLL 65MARAKNQPYQKLITTTGIKFKLDLSEEEGKRFDEYFSEYAKAVNFCAKVIYQLRKNLKFAGKKELAAKEWKFEISNCDFCNKQKEIYYKNIANGQKVCKGCHRTNFSDNAIRKKMIPVKGRKVESKFNIHNTTKKISGTHRHWAFEDAADIIESMDKQRKEKQKRLRREKRKLSYFFELFGDPAKRYELPKVGKQRVPRYLHKIIDKDSLTKKRGYSLSYIKNKIKISERNIERDEKS LRKASPIAFGARKIKMSKLDPKRAFDLENNVFKIPGKVIKGQYKFFGTNVANEHGKKFYKDRISKILAGKPKYFYLLRKKVAESDGNPIFEYYVQWSIDTETPAITSYDNILGIDAGITNLATTVLIPKNLSAEHCSHCGNNHVKPIFTKFFSGKELKAIKIKSRKQKYFLRGKHNKLVKIK RIRPIEQKVDGYCHVVSKQIVEMAKERNSCIALEKLEKPKKSKFRQRRREKYAVSMFVFKKLATFIKYKAAREGIEIIPVEPEGTSYTCSHCKNAQNNQRPYFKPNSKKSWTSMFKCGK CGIELNSDYNAAFNIAQKALNMTSA 66MDEKHFFCSYCNKELKISKNLINKISKGSIREDEAVSKAISIHNKKEHSLILGIKFKLFIENKLDKKKLNEYFDNYSKAVTFAARIFDKIRSPYKFIGLKDKNTKKWTFPKAKCVFCLEEKEVAYANEKDNSKICTECYLKEFGENGIRKKIYSTRGRKVEPKYNIFNSTKELSSTHYNYAIRDAFQLLDALKKQRQKKLKSIFNQKLRLKEFEDIFSDPQKRIELSLKPHQREKRYIHLSKSGQESINRGYTLRFVRGKIKSLTRNIEREEKSLRKKTPIHFKGNRLMIFPAGIKFDFASNKVKISISKNLPNEFNFSGTNVKNEHGKSFFKSRIELIKTQKPKYAYVLRKIKREYSKLRNYEIEKIRLENPNADLCDFYLQYTIETESRNNEEINGIIGIDRGITNLACLVLLKKGDKKPSGVKFYK GNKILGMKIAYRKHLYLLKGKRNKLRKQRQIRAIEPKINLILHQISKDIVKIAKEKNFAIALEQLEKPKKARFAQRKKEKYKLALFTFKNLSTLIEYKSKREGIPVIYVPPEKTSQMCSHCAINGDEHVDTQRPYKKPNAQKPSYSLFKCNKCGIELNADYNAAFNIAQKGLKTLMLNHSH 67MLQTLLVKLDPSKEQYKMLYETMERFNEACNQIAETVFAIHSANKIEVQKTVYYPIREKFGLSAQLTILAIRKVCEAYKRDKSIKPEFRLDGALVYDQRVLSWKGLDKVSLVTLQGRQIIPIKFGDYQKARMDRIRGQADLILVKGVFYLCVVVEVSEESPYDPKGVLGVDLGIKNLAVDSDGEVHSGEQTTNTRERLDSLKARLQSKGTKSAKRHLKKLSGRMAKFSKDVNHCISK KLVAKAKGTLMSIALEDLQGIRDRVTVRKAQRRNLHTWNFGLLRMFVDYKAKIAGVPLVFVDPRNTSRTCPSCGHVAKANRPTRDEFRCVSCGFAGAADHIAAMNIAFRAEVSQPIVTRFFVQSQAPSFRVG 68MDEEPDSAEPNLAPISVKLKLVKLDGEKLAALNDYFNEYAKAVNFCELKMQKIRKNLVNIRGTYLKEKKAWINQTGECCICKKIDELRCEDKNPDINGKICKKCYNGRYGNQMIRKLFVSTNKRAVPKSLDIRKVARLHNTHYHRIPPEAADIIKAIETAERKRRNRILFDERRYNELK DALENEEKRVARPKKPKEREVRYVPISKKDTPSKGYTMNALVRKVSGMAKKIERAKRNLNKRKKIEYLGRRILLDKNWVRFDFDKSEISIPTMKEFFGEMRFEITGPSNVMSPNGREYFTKWFDRIKAQPDNYCYLLRKESEDETDFYLQYTWRPDAHPKKDYTGCLGIDIGGSKLAS AVYFDADKNRAKQPIQIFSNPIGKWKTKRQKVIKVLSKAAVRHKTKKLESLRNIEPRIDVHCHRIARKIVGMALAANAFISMENLEGGIREKQKAKETKKQKFSRNMFVFRKLSKLIEYKALMEGVKVVYIVPDYTSQLCSSCGTNNTKRPKQAIFMCQNTECRYFGKNINADFNAAINIAKKALNRKDIVRELS  69MEKNNSEQTSITTGIKFKLKLDKETKEKLNNYFDEYGKAINFAVRIIQMQLNDDRLAGK YKRDEKGKPILGEDGKKILEIPNDFCSCGNQVNHYVNGVSFCQECYKKRFSENGIRKRMYSAKGRKAEQDINIKNSTNKISKTHFNYAIREAFNLDKSIKKQREKRFKKLKDMKRKLQEFLEIRDGKRVICPKIEKQKVERYIHPSWINKEKKLEEFRGYSLSIVNSKIKSFDRNIQREEKSLKEKGQINFKAQRLMLDKSVKFLKDNKVSFTISKELPKTFELDLPKKEKKLNWLNEKLEIIKNQKPKYAYLLRKENNIFLQYTLDSIPEIHSEYSGAVGIDRGVSHIAVYTFLDKDGKNERPFFLSSSGILRLKNLQKERDKFLRKKHNKIRKKGNMRNIEQKINLILHEYSKQIVNFAKDK NAFIVFELLEKPKKSRERMSKKIQYKLSQFTFKKLSDLVDYKAKREGIKVIYVEPAYTSK DCSHCGERVNTQRPFNGNFSLFKCNKCGIVLNSDYNASLNIARKGLNISAN 70MAEEKFFFCEKCNKDIKIPKNYINKQGAEEKARAKHEHRVHALILGIKFKIYPKKEDISKLNDYFDEYAKAVTFTAKIVDKLKAPFLFAGKRDKDTSKKKWVFPVDKCSFCKEKTEINYRTKQGKNICNSCYLTEFGEQGLLEKIYATKGRKVSSSFNLFNSTKKLTGTHNNYVVKESLQLLDALKKQRSKRLKKLSNTRRKLKQFEEMFEKEDKRFQLPLKEKQRELRFIHVSQKDRATEFKGYTMNKIKSKIKVLRRNIEREQRSLNRKSPVFFRGTRIRLSPSVQFDDKDNKIKLTLSKELPKEYSFSGLNVANEHGRKFFAEKLKLIKENKSKYAYLLRRQVNKNNKKPIYDYYLQYTVEFLPNIITNYNGILGIDRGINTLACIVLLENKKEKPSFVKFFSGKGILNLKNKRRKQLYFLKGVHNKYRKQQKIRPIEPRIDQILHDISKQIIDLAKEKRVAISLEQLEKPQKPKFRQSRKAKYKLSQFNFKTLSNYIDYKAKKEGIRVIYIAPEMTSQNCSRCAMKNDLHVNTQRPYK NTSSLFKCNKCGVELNADYNAAFNIAQKGLKILNS  71MISLKLKLLPDEEQKKLLDEMFWKWASICTRVGFGRADKEDLKPPKDAEGVWFSLTQLNQANTDINDLREAMKHQKHRLEYEKNRLEAQRDDTQDALKNPDRREISTKRKDLFRPK ASVEKGFLKLKYHQERYWVRRLKEINKLIERKTKTLIKIEKGRIKFKATRITLHQGSFKIRFGDKPAFLIKALSGKNQIDAPFVVVPEQPICGSVVNSKKYLDEITTNFLAYSVNAMLFGLS RSEEMLLKAKRPEKIKKKEEKLAKKQSAFENKKKELQKLLGRELTQQEEAIIEETRNQFFQDFEVKITKQYSELLSKIANELKQKNDFLKVNKYPILLRKPLKKAKSKKINNLSPSEWKYYLQFGVKPLLKQKSRRKSRNVLGIDRGLKHLLAVTVLEPDKKTFVWNKLYPNPITGWK WRRRKLLRSLKRLKRRIKSQKHETIHENQTRKKLKSLQGRIDDLLHNISRKIVETAKEYDAVIVVEDLQSMRQHGRSKGNRLKTLNYALSLFDYANVMQLIKYKAGIEGIQIYDVKPAGTSQNCAYCLLAQRDSHEYKRSQENSKIGVCLNPNCQNHKKQIDADLNAARVIASCYALK INDSQPFGTRKRFKKRTTN 72METLSLKLKLNPSKEQLLVLDKMFWKWASICTRLGLKKAEMSDLEPPKDAEGVWFSKTQLNQANTDVNDLRKAMQHQGKRIEYELDKVENRRNEIQEMLEKPDRRDISPNRKDLFRPKAAVEKGYLKLKYHKLGYWSKELKTANKLIERKRKTLAKIDAGKMKFKPTRISLHTNSFRIKFGEEPKIALSTTSKHEKIELPLITSLQRPLKTSCAKKSKTYLDAAILNFLAYSTNAALFGLSRSEEMLLKAKKPEKIEKRDRKLATKRESFDKKLKTLEKLLERKLSEKEKSVFKRKQTEFFDKFCITLDETYVEALHRIAEELVSKNKYLEIKKYPVLLRKPESRLRSKKLKNLKPEDWTYYIQFGFQPLLDTPKPIKTKTVLGIDRGVRHLLAVSIFDPRTKTFTFNRLYSNPIVDWK WRRRKLLRSIKRLKRRLKSEKHVHLHENQFKAKLRSLEGRIEDHFHNLSKEIVDLAKENNSVIVVENLGGMRQHGRGRGKWLKALNYALSHFDYAKVMQLIKYKAELAGVFVYDVAPAGTSINCAYCLLNDKDASNYTRGKVINGKKNTKIGECKTCKKEFDADLNAARVIALCYEKRLNDPQPFGTRKQFKPKKP 73MKALKLQLIPTRKQYKILDEMFWKWASLANRVSQKGESKETLAPKKDIQKIQFNATQLNQIEKDIKDLRGAMKEQQKQKERLLLQIQERRSTISEMLNDDNNKERDPHRPLNFRPKGWRKFHTSKHWVGELSKILRQEDRVKKTIERIVAGKISFKPKRIGIWSSNYKINFFKRKISINPLNSKGFELTLMTEPTQDLIGKNGGKSVLNNKRYLDDSIKSLLMFALHSRFFGLNNTDTYLLGGKINPSLVKYYKKNQDMGEFGREIVEKFERKLKQEINEQQKKIIMSQIKEQYSNRDSAFNKDYLGLINEFSEVFNQRKSERAEYLLDSFEDKIKQIKQEIGESLNISDWDFLIDEAKKAYGYEEGFTEYVYSKRYLEILNKIVKAVLITDIYFDLRKYPILLRKPLDKIKKISNLKPDEWS YYIQFGYDSINPVQLMSTDKFLGIDRGLTHLLAYSVFDKEKKEFIINQLEPNPIMGWKWK LRKVKRSLQHLERRIRAQKMVKLPENQMKKKLKSIEPKIEVHYHNISRKIVNLAKDYNASIVVESLEGGGLKQHGRKKNARNRSLNYALSLFDYGKIASLIKYKADLEGVPMYEVLPAYTSQQCAKCVLEKGSFVDPEIIGYVEDIGIKGSLLDSLFEGTELSSIQVLKKIKNKIELSARDNHNKEINLILKYNFKGLVIVRGQDKEEIAEHPIKEINGKFAILDFVYKRGKEKVGKKGNQKVRYTGNKKVGYCSKHGQVDADLNASRVIALCKYLDINDPILFGEQRKSFK  74MVTRAIKLKLDPTKNQYKLLNEMFWKWASLANRFSQKGASKETLAPKDGTQKIQFNATQLNQIKKDVDDLRGAMEKQGKQKERLLIQIQERLLTISEILRDDSKKEKDPHRPQNFRPFGWRRFHTSAYWSSEASKLTRQVDRVRRTIERIKAGKINFKPKRIGLWSSTYKINFLKKKINISPLKSKSFELDLITEPQQKIIGKEGGKSVANSKKYLDDSIKSLLIFAIKSRLFGLNNKDKPLFENIITPNLVRYHKKGQEQENFKKEVIKKFENKLKKEISQKQKEIIFSQIERQYENRDATFSEDYLRAISEFSEIFNQRKKERAKELLNSFNEKIRQLKKEVNGNISEEDLKILEVEAEKAYNYENGFIEWEYSEQFLGVLEKIARAVLISDNYFDLKKYPILIRKPTNKSKKITNLKPEEWDYYIQFGYGLINSPMKIETKNFMGIDRGLTHLLAYSIFDRDSEKFTINQLELNPIKGWKWKLRKVKRSLQHLERRMRAQKGVKLPENQMKKRLKSIEPKIESYYHNLSRKIVNLAKANNAS IVVESLEGGGLKQHGRKKNSRHRALNYALSLFDYGKIASLIKYKSDLEGVPMYEVLPAYTSQQCAKCVLKKGSFVEPEIIGYIEEIGFKENLLTLLFEDTGLSSVQVLKKSKNKMTLSARDKEGKMVDLVLKYNFKGLVISQEKKKEEIVEFPIKEIDGKFAVLDSAYKRGKERISKKGNQKLVYTGNKKVGYCSVHGQVDADLNASRVIALCKYLGINEPIVFGEQRKSFK  75LDLITEPIQPHKSSSLRSKEFLEYQISDFLNFSLHSLFFGLASNEGPLVDFKIYDKIVIPKPEERFPKKESEEGKKLDSFDKRVEEYYSDKLEKKIERKLNTEEKNVIDREKTRIWGEVNKLEEIRSIIDEINEIKKQKHISEKSKLLGEKWKKVNNIQETLLSQEYVSLISNLSDELTNKKKELLAKKYSKFDDKIKKIKEDYGLEFDENTIKKEGEKAFLNPDKFSKYQFSSSYLKLIGEIARSLITYKGFLDLNKYPIIFRKPINKVKKIHNLEPDEWKYYIQFGYEQINNPKLETENILGIDRGLTHILAYSVFEPRSSKFILNKLEPNPIEGWKWKLRKLRRSIQNLERRWRAQDNVKLPENQMKKNLRSIEDKVENLYHNLSRKIVDLAKEKNACIVFEKLEGQGMKQHGRKKSDRLRGLNYKLSLFDYGKIAKLIKYKAEIEGIPIYRIDSAYTSQNCAKCVLESRRFAQPEEISCLDDFKEGDNLDKRILEGTGLVEAKIYKKLLKEKKEDFEIEEDIAMFDTKKVIKENKEKTVILDYVYTRRKEIIGTNHKKNIKGIAKYTGNTKIGYCMKHGQVDADLNASRTIALCKNFDINNPEIWK 76MSDESLVSSEDKLAIKIKIVPNAEQAKMLDEMFKKWSSICNRISRGKEDIETLRPDEGKELQFNSTQLNSATMDVSDLKKAMARQGERLEAEVSKLRGRYETIDASLRDPSRRHTNPQKPSSFYPSDWDISGRLTPRFHTARHYSTELRKLKAKEDKMLKTINKIKNGKIVFKPKRITLWPSSVNMAFKGSRLLLKPFANGFEMELPIVISPQKTADGKSQKASAEYMRNALLGLAGYSINQLLFGMNRSQKMLANAKKPEKVEKFLEQMKNKDANFDKKIKALEGKWLLDRKLKESEKSSIAVVRTKFFKSGKVELNEDYLKLLKHMANEILERDGFVNLNKYPILSRKPMKRYKQKNIDNLKPNMWKYYIQFGYEPIFERKASGKPKNIMGIDRGLTHLLAVAVFSPDQQKFLFNHLESNPIMHWKWKLRKIRRSIQHMERRIRAEKNKHIHEAQLKKRLGSIEEKTEQHYHIVS SKIINWAIEYEAAIVLESLSHMKQRGGKKSVRTRALNYALSLFDYEKVARLITYKARIRGIPVYDVLPGMTSKTCATCLLNGSQGAYVRGLETTKAAGKATKRKNMKIGKCMVCNSSENSMIDADLNAARVIAICKYKNLNDPQPAGSRKVFKRF 77MLALKLKIMPTEKQAEILDAMFWKWASICSRIAKMKKKVSVKENKKELSKKIPSNSDIWFSKTQLCQAEVDVGDHKKALKNFEKRQESLLDELKYKVKAINEVINDESKREIDPNNPS KFRIKDSTKKGNLNSPKFFTLKKWQKILQENEKRIKKKESTIEKLKRGNIFFNPTKISLHEEEYSINFGSSKLUNCFYKYNKKSGINSDQLENKFNEFQNGLNIICSPLQPIRGSSKRSFEFIRNSIINFLMYSLYAKLFGIPRSVKALMKSNKDENKLKLEEKLKKKKSSFNKTVKEFEKMIGRKLSDNESKILNDESKKFFEIIKSNNKYIPSEEYLKLLKDISEEIYNSNIDFKPYKYSILIRKPLSKFKSKKLYNLKPTDYKYYLQLSYEPFSKQLIATKTILGIDRGLKHLLAVSVFDPSQNKFVYNKLIKNPVFKWKKRYHDLKRSIRNRERRIRALTGVHIHENQLIKKLKSMKNKINVLYHNVSKNIVDLAKKYESTIVLERLENLKQHGRSKGKRYKKLNYVLSNFDYKKIESLISYKAKKEGVPVSNINPKYTSKTCAKCLLEVNQLSELKNEYNRDSKNSKIGICNIHGQIDADLNAARVIALCYSKNLNEPHFK  78VINLFGYKFALYPNKTQEELLNKHLGECGWLYNKAIEQNEYYKADSNIEEAQKKFELLPDKNSDEAKVLRGNISKDNYVYRTLVKKKKSEINVQIRKAVVLRPAETIRNLAKVKKKGLSVGRLKFIPIREWDVLPFKQSDQIRLEENYLILEPYGRLKFKMHRPLLGKPKTFCIKRTATDRWTISFSTEYDDSNMRKNDGGQVGIDVGLKTHLRLSNENPDEDPRYPNPKIWKRYDRRLTILQRRISKSKKLGKNRTRLRLRLSRLWEKIRNSRADLIQNETYEILSENKLIAIEDLNVK GMQEKKDKKGRKGRTRAQEKGLHRSISDAAFSEFRRVLEYKAKRFGSEVKPVSAIDSSK ECHNCGNKKGMPLESRIYECPKCGLKIDRDLNSAKVILARATGVRPGSNARADTKISATAGASVQTEGTVSEDFRQQMETSDQKPMQGEGSKEPPMNPEHKSSGRGSKHVNIGCKNKVGLYNEDENSRSTEKQIMDENRSTTEDMVEIGALHSPVLTT 79MIASIDYEAVSQALIVFEFKAKGKDSQYQAIDEAIRSYRFIRNSCLRYWMDNKKVGKYDLNKYCKVLAKQYPFANKLNSQARQSAAECSWSAISRFYDNCKRKVSGKKGFPKFKKHARSVEYKTSGWKLSENRKAITFTDKNGIGKLKLKGTYDLHFSQLEDMKRVRLVRRADGYYVQFCISVDVKVETEPTGKAIGLDVGIKYFLADSSGNTIENPQFYRKAEKKLNRANRRKS KKYIRGVKPQSKNYHKARCRYARKHLRVSRQRKEYCKRVAYCVIHSNDVVAYEDLNVKGMVKNRHLAKSISDVAWSTFRHWLEYFAIKYGKLTIPVAPHNTSQNCSNCDKKVPKSLSTRTHICHHCGYSEDRDVNAAKNILKKALSTVGQTGSLKLGEIEPLLVLEQSCTRKFDL 80LAEENTLHLTLAMSLPLNDLPENRTRSELWRRQWLPQKKLSLLLGVNQSVRKAAADCLRWFEPYQELLWWEPTDPDGKKLLDKEGRPIKRTAGHMRVLRKLEEIAPFRGYQLGSAVKNGLRHKVADLLLSYAKRKLDPQFTDKTSYPSIGDQFPIVWTGAFVCYEQSITGQLYLYLPLFPRGSHQEDITNNYDPDRGPALQVFGEKEIARLSRSTSGLLLPLQFDKWGEATFIRGENNPPTWKATHRRSDKKWLSEVLLREKDFQPKRVELLVRNGRIFVNVACEIPTKPLLEVENFMGVSFGLEHLVTVVVINRDGNVVHQRQEPARRYEKTYFARLERLRRRGGPFSQELETFHYRQVAQIVEEALRFKSVPAVEQVGNIPKGRYNPRLNLRLSYWPFGKLADLTSYKAVKEGLPKPYSVYSATAKMLCSTCGAANKEGDQPISLKGPTVYCGNCGTRHNTGFNTALNLARR AQELFVKGVVAR81 MSQSLLKWHDMAGRDKDASRSLQKSAVEGVLLHLTASHRVALEMLEKSVSQTVAVTMEAAQQRLVIVLEDDPTKATSRKRVISADLQFTREEFGSLPNWAQKLASTCPEIATKYADK HINSIRIAWGVAKESTNGDAVEQKLQWQIRLLDVTMFLQQLVLQLADKALLEQIPSSIRGGIGQEVAQQVTSHIQLLDSGTVLKAELPTISDRNSELARKQWEDAIQTVCTYALPFSRERARILDPGKYAAEDPRGDRLINIDPMWARVLKGPTVKSLPLLFVSGSSIRIVKLTLPRKHAAGHKHTFTATYLVLPVSREWINSLPGTVQEKVQWWKKPDVLATQELLVGKGALKKSANTLVIPISAGKKRFFNHILPALQRGFPLQWQRIVGRSYRRPATHRKWFAQLTIGYTNPSSLPEMALGIHFGMKDILWWALADKQGNILKDGSIPGNSILDFSLQEKGKIERQQKAGKNVAGK KYGKSLLNATYRVVNGVLEFSKGISAEHASQPIGLGLETIRFVDKASGSSPVNARHSNWNYGQLSGIFANKAGPAGFSVTEITLKKAQRDLSDAEQARVLAIEATKRFASRIKRLATKRK  DDTLFV 82VEPVEKERFYYRTYTFRLDGQPRTQNLTTQSGWGLLTKAVLDNTKHYWEIVHHARIANQPIVFENPVIDEQGNPKLNKLGQPRFWKRPISDIVNQLRALFENQNPYQLGSSLIQGTYWDVAENLASWYALNKEYLAGTATWGEPSFPEPHPLTEINQWMPLTFSSGKVVRLLKNAS GRYFIGLPILGENNPCYRMRTIEKLIPCDGKGRVTSGSLILFPLVGIYAQQHRRMTDICESIRTEKGKLAWAQVSIDYVREVDKRRRMRRTRKSQGWIQGPWQEVFILRLVLAHKAPKLYKPRCFAGISLGPKTLASCVILDQDERVVEKQQWSGSELLSLIHQGEERLRSLREQSKPTWNAAYRKQLKSLINTQVFTIVTFLRERGAAVRLESIARVRKSTPAPPVNFLLSHWAYRQITERLKDLAIRNGMPLTHSNGSYGVRFTCSQCGATNQGIKDPTKYKVDIESETFLCSICSHREIAAVNTATNLAKQLLDE 83MNDTETSETLTSHRTVCAHLHVVGETGSLPRLVEAALAELITLNGRATQALLSLAKNGLVLRRDKEENLIAAELTLPCRKNKYADVAAKAGEPILATRINNKGKLVTKKWYGEGNSYHIVRFTPETGMFTVRVFDRYAFDEELLHLHSEVVFGSDLPKGIKAKTDSLPANFLQAVFTSFLELPFQGFPDIVVKPAMKQAAEQLLSYVQLEAGENQQAEYPDTNERDPELRLVEWQK SLHELSVRTEPFEFVRARDIDYYAETDRRGNRFVNITPEWTKFAESPFARRLPLKIPPEFCILLRRKTEGHAKIPNRIYLGLQIFDGVTPDSTLGVLATAEDGKLFWWHDHLDEFSNLEGK PEPKLKNKPQLLMVSLEYDREQRFEESVGGDRKICLVTLKETRNFRRGWNGRILGIHFQHNPVITWALMDHDAEVLEKGFIEGNAFLGKALDKQALNEYLQKGGKWVGDRSFGNKLK GITHTLASLIVRLAREKDAWIALEEISWVQKQSADSVANHEIVEQPHHSLTR 84MNDTETSETLTSHRTVCAHLHVVGETGSLPRLVEAALAELITLNGRATQALLSLAKNGLVLRRDKEENLIAAELTLPCRKNKYADVAAKAGEPILATRINNKGKLVTKKWYGEGNSYHIVRFTPETGMFTVRVFDRYAFDEELLHLHSEVVFGSDLPKGIKAKTDSLPANFLQAVFTSFLELPFQGFPDIVVKPAMKQAAEQLLSYVQLEAGENQQAEYPDTNERDPELRLVEWQK SLHELSVRTEPFEFVRARDIDYYAETDRRGNRFVNITPEWTKFAESPFARRLPLKIPPEFCILLRRKTEGHAKIPNRIYLGLQIFDGVTPDSTLGVLATAEDGKLFWWHDHLDEFSNLEGK PEPKLKNKPQLLMVSLEYDREQRFEESVGGDRKICLVTLKETRNFRRGRHGHTRTDRLPAGNTLWRADFATSAEVAAPKWNGRILGIHFQHNPVITWALMDHDAEVLEKGFIEGNAFLGKALDKQALNEYLQKGGKWVGDRSFGNKLKGITHTLASLIVRLAREKDAWIALEEIS WVQKQSADSVANRRFSMWNYSRLATLIEWLGTDIATRDCGTAAPLAHKVSDYLTHFTCPECGACRKAGQKKEIADTVRAGDILTCRKCGFSGPIPDNFIAEFVAKKALERMLKKKPV 85MAKRNFGEKSEALYRAVRFEVRPSKEELSILLAVSEVLRMLFNSALAERQQVFTEFIASLYAELKSASVPEEISEIRKKLREAYKEHSISLFDQINALTARRVEDEAFASVTRNWQEETLDALDGAYKSFLSLRRKGDYDAHSPRSRDSGFFQKIPGRSGFKIGEGRIALSCGAGRKLSFPIPDYQQGRLAETTKLKKFELYRDQPNLAKSGRFWISVVYELPKPEATTCQSEQVAFVALGASSIGVVSQRGEEVIALWRSDKHWVPKIEAVEERMKRRVKGSRGWLRLLNSGKRRMHMISSRQHVQDEREIVDYLVRNHGSHFVVTELVVRSKEGKLADSSKPERGGSLGLNWAAQNTGSLSRLVRQLEEKVKEHGGSVRKHKLTLTEAPPARGAENKLWMARKLRESFLKEV 86LAKNDEKELLYQSVKFEIYPDESKIRVLTRVSNILVLVWNSALGERRARFELYIAPLYEELKKFPRKSAESNALRQKIREGYKEHIPTFFDQLKKLLTPMRKEDPALLGSVPRAYQEETLNTLNGSFVSFMTLRRNNDMDAKPPKGRAEDRFHEISGRSGFKIDGSEFVLSTKEQKLRFPIPNYQLEKLKEAKQIKKFTLYQSRDRRFWISIAYEIELPDQRPFNPEEVIYIAFGASSIGVISPEGEKVIDFWRPDKHWKPKIKEVENRMRSCKKGSRAWKKRAAARRKMYAMTQRQQKLNFIREIVASLLRLGFHFVVTEYTVRSKPGKLADGSNPKRGGAPQGFNWSAQNTGSFGEFILWLKQKVKEQGGTVQTFRLVLGQSERPEKRGRDNKIEMVRLLREKYLESQTIVV 87MAKGKKKEGKPLYRAVRFEIFPTSDQITLFLRVSKNLQQVWNEAWQERQSCYEQFFGSIYERIGQAKKRAQEAGFSEVWENEAKKGLNKKLRQQEISMQLVSEKESLLQELSIAFQEHGVTLYDQINGLTARRIIGEFALIPRNWQEETLDSLDGSFKSFLALRKNGDPDAKPPRQRVS ENSFYKIPGRSGFKVSNGQIYLSFGKIGQTLTSVIPEFQLKRLETAIKLKKFELCRDERDMAKPGRFWISVAYEIPKPEKVPVVSKQITYLAIGASRLGVVSPKGEFCLNLPRSDYHWKPQINALQERLEGVVKGSRKWKKRMAACTRMFAKLGHQQKQHGQYEVVKKLLRHGVHFVVTELKVRSKPGALADASKSDRKGSPTGPNWSAQNTGNIARLIQKLTDKASEHGGTVIKRNPPLLSLEERQLPDAQRKIFIAKKLREEFLADQK  88MAKREKKDDVVLRGTKMRIYPTDRQVTLMDMWRRRCISLWNLLLNLETAAYGAKNTRSKLGWRSIWARVVEENHAKALIVYQHGKCKKDGSFVLKRDGTVKHPPRERFPGDRKILLGLFDALRHTLDKGAKCKCNVNQPYALTRAWLDETGHGARTADIIAWLKDFKGECDCTAISTAAKYCPAPPTAELLTKIKRAAPADDLPVDQAILLDLFGALRGGLKQKECDHTHARTVAYFEKHELAGRAEDILAWLIAHGGTCDCKIVEEAANHCPGPRLFIWEHELAMIMARLK AEPRTEWIGDLPSHAAQTVVKDLVKALQTMLKERAKAAAGDESARKTGFPKFKKQAYAAGSVYFPNTTMFFDVAAGRVQLPNGCGSMRCEIPRQLVAELLERNLKPGLVIGAQLGLLGGRIWRQGDRWYLSCQWERPQPTLLPKTGRTAGVKIAASIVFTTYDNRGQTKEYPMPPADKKLTAVHLVAGKQNSRALEAQKEKEKKLKARKERLRLGKLEKGHDPNALKPLKRPRVRRSKLFYKSAARLAACEAIERDRRDGFLHRVTNEIVHKFDAVSVQKMSVAPMMRRQKQKEKQIESKKNEAKKEDNGAAKKPRNLKPVRKLLRHVAMARGRQFLEYKYNDLRGPGSVLIADRLEPEVQECSRCGTKNPQMKDGRRLLRCIGVLPDGTDCDAVLPRNRNAARNAEKRLRKHREAHNA 89MNEVLPIPAVGEDAADTIMRGSKMRIYPSVRQAATMDLWRRRCIQLWNLLLELEQAAYSGENRRTQIGWRSIWATVVEDSHAEAVRVAREGKKRKDGTFRKAPSGKEIPPLDPAMLAKIQRQMNGAVDVDPKTGEVTPAQPRLFMWEHELQKIMARLKQAPRTHWIDDLPSHAAQSVVKDLIKALQAMLRERKKRASGIGGRDTGFPKFKKNRYAAGSVYFANTQLRFEAKRGKAGDPDAVRGEFARVKLPNGVGWMECRMPRHINAAHAYAQATLMGGRIWRQGENWYLSCQWKMPKPAPLPRAGRTAAIKIAAAIPITTVDNRGQTREYAMPPIDRERIAAHAAAGRAQSRALEARKRRAKKREAYAKKRHAKKLERGIAAKPPGRARIKLSPGFYAAAAKLAKLEAEDANAREAWLHEITTQIVRNFDVIAVPRMEVAKLMKKPEPPEEKEEQVKAPWQGKRRSLKAARVMMRRTAMALIQTTLKYKAVDLRGPQAYEEIAPLDVTAAACSGCGVLKPEWKMARAKGREIMRCQEPLPGGKTCNTVLTYTRNSARVIGRELAVRLAERQKA 90MTTQKTYNFCFYDQRFFELSKEAGEVYSRSLEEFWKIYDETGVWLSKFDLQKHMRNKLERKLLHSDSFLGAMQQVHANLASWKQAKKVVPDACPPRKPKFLQAILFKKSQIKYKNGFLRLTLGTEKEFLYLKWDINIPLPIYGSVTYSKTRGWKINLCLETEVEQKNLSENKYLSIDLGVKRVATIFDGENTITLSGKKFMGLMHYRNKLNGKTQSRLSHKKKGSNNYKKIQRAK RKTTDRLLNIQKEMLHKYSSFIVNYAIRNDIGNIIIGDNSSTHDSPNMRGKTNQKISQNPEQKLKNYIKYKFESISGRVDIVPEPYTSRKCPHCKNIKKSSPKGRTYKCKKCGFIFDRDGVGAINIYNENVSFGQIISPGRIRSLTEPIGMKFHNEIYFKSYVAA 91MSVRSFQARVECDKQTMEHLWRTHKVFNERLPEIIKILFKMKRGECGQNDKQKSLYKSISQSILEANAQNADYLLNSVSIKGWKPGTAKKYRNASFTWADDAAKLSSQGIHVYDKKQVLGDLPGMMSQMVCRQSVEAISGHIELTKKWEKEHNEWLKEKEKWESEDEHKKYLDLREKFEQFEQSIGGKITKRRGRWHLYLKWLSDNPDFAAWRGNKAVINPLSEKAQIRINKAKPNKKNSVERDEFFKANPEMKALDNLHGYYERNFVRRRKTKKNPDGFDHKPTFTLPHPTIHPRWFVFNKPKTNPEGYRKLILPKKAGDLGSLEMRLLTGEKNKGNYPDDWISVKFKADPRLSLIRPVKGRRVVRKGKEQGQTKETDSYEFFDKHLKKWRPAKLSGVKLIFPDKTPK AAYLYFTCDIPDEPLTETAKKIQWLETGDVTKKGKKRKKKVLPHGLVSCAVDLSMRRGTTGFATLCRYENGKIHILRSRNLWVGYKEGKGCHPYRWTEGPDLGHIAKHKREIRILRSK RGKPVKGEESHIDLQKHIDYMGEDRFKKAARTIVNFALNTENAASKNGFYPRADVLLLENLEGLIPDAEKERGINRALAGWNRRHLVERVIEMAKDAGFKRRVFEIPPYGTSQVCSKCGALGRRYSIIRENNRREIRFGYVEKLFACPNCGYCANADHNASVNLNRRFLIEDSFKSYYDWKRLSEKKQKEEIETIESKLMDKLCAMHKISRGSISK  92MHLWRTHCVFNQRLPALLKRLFAMRRGEVGGNEAQRQVYQRVAQFVLARDAKDSVDLLNAVSLRKRSANSAFKKKATISCNGQAREVTGEEVFAEAVALASKGVFAYDKDDMRAGLPDSLFQPLTRDAVACMRSHEELVATWKKEYREWRDRKSEWEAEPEHALYLNLRPKFEEGEAARGGRFRKRAERDHAYLDWLEANPQLAAWRRKAPPAVVPIDEAGKRRIARAKAWKQASVRAEEFWKRNPELHALHKIHVQYLREFVRPRRTRRNKRREGFKQRPTFTMPDPVRHPRWCLFNAPQTSPQGYRLLRLPQSRRTVGSVELRLLTGPSDGAGFPDAWVNVRFKADPRLAQLRPVKVPRTVTRGKNKGAKVEADGFRYYDDQLLIERDAQVSGVKLLFRDIRMAPFADKPIEDRLLSATPYLVFAVEIKDEARTERAKAIRFDETSELTKSGKKRKTLPAGLVS VAVDLDTRGVGFLTRAVIGVPEIQQTHHGVRLLQSRYVAVGQVEARASGEAEWSPGPDLAHIARHKREIRRLRQLRGKPVKGERSHVRLQAHIDRMGEDRFKKAARKIVNEALRGSNPAAGDPYTRADVLLYESLETLLPDAERERGINRALLRWNRAKLIEHLKRMCDDAGIRHFPVSPFGTSQVCSKCGALGRRYSLARENGRAVIRFGWVERLFACPNPECPGRRPDRPDRPFTCNSDHNASVNLHRVFALGDQAVAAFRALAPRDSPARTLAVKRVEDTLRPQLMRVHKL ADAGVDSPF 93MATLVYRYGVRAHGSARQQDAVVSDPAMLEQLRLGHELRNALVGVQHRYEDGKRAVWSGFASVAAADHRVTTGETAVAELEKQARAEHSADRTAATRQGTAESLKAARAAVKQARADRKAAMAAVAEQAKPKIQALGDDRDAEIKDLYRRFCQDGVLLPRCGRCAGDLRS DGDCTDCGAAHEPRKLYWATYNAIREDHQTAVKLVEAKRKAGQPARLRFRRWTGDGTLTVQLQRMHGPACRCVTCAEKLTRRARKTDPQAPAVAADPAYPPTDPPRDPALLASGQGKWRNVLQLGTWIPPGEWSAMSRAERRRVGRSHIGWQLGGGRQLTLPVQLHRQMPADADVAMAQLTRVRVGGRHRMSVALTAKLPDPPQVQGLPPVALHLGWRQRPDGSLRVATWACPQPLDLPPAVADVVVSHGGRWGEVIMPARWLADAEVPPRLLGRRDKAMEPVLEALADWLEAHTEACTARMTPALVRRWRSQGRLAGLTNRWRGQPPTGSAEILTYLEAWRIQDKLLWERESHLRRRLAARRDDAWRRVASWLARHAGVLVVDDADIAELRRRDDPADTDPTMPASAAQAARARAALAAPGRLRHLATITATRDGLGVHTVASAGLTRLHRKCGHQAQPDPRYAASAVVTCPGCGNGYDQDYNAAMLMLDRQQQP 94MSRVELHRAYKFRLYPTPAQVAELAEWERQLRRLYNLAHSQRLAAMQRHVRPKSPGVLKSECLSCGAVAVAEIGTDGKAKKTVKHAVGCSVLECRSCGGSPDAEGRTAHTAACSFVDYYRQGREMTQLLEEDDQLARVVCSARQETLRDLEKAWQRWHKMPGFGKPHFKKRIDSCRIYFSTPKSWAVDLGYLSFTGVASSVGRIKIRQDRVWPGDAKFSSCHVVRDVDEWYAVFPLTFTKEIEKPKGGAVGINRGAVHAIADSTGRVVDSPKFYARSLGVIRHRARLLDRKVPFGRAVKPSPTKYHGLPKADIDAAAARVNASPGRLVYEARARGSIAAAEAHLAALVLPAPRQTSQLPSEGRNRERARRFLALAHQRVRRQREWFLHNESAHYAQSYTKIAIEDWSTKEMTSSEPRDAEEMKRVTRARNRSILDVGWYELGRQIAYKSEATGAEFAKVDPGLRETETHVPEAIVRERDVDVSGMLRGEAGISGTCSRCGGLLRASASGHADAECEVCLHVEVGDVNAAVNVLKRAMFPGAAPPSKEKAKVTIGIKGRKKKRAA 95MSRVELHRAYKFRLYPTPVQVAELSEWERQLRRLYNLGHEQRLLTLTRHLRPKSPGVLK GECLSCDSTQVQEVGADGRPKTTVRHAEQCPTLACRSCGALRDAEGRTAHTVACAFVDYYRQGREMTELLAADDQLARVVCSARQEVLRDLDKAWQRWRKMPGFGKPRFKRRTDSCRIYFSTPKAWKLEGGHLSFTGAATTVGAIKMRQDRNWPASVQFSSCHVVRDVDEWYAVFPLTFVAEVARPKGGAVGINRGAVHAIADSTGRVVDSPRYYARALGVIRHRARLFDRKVPSGHAVKPSPTKYRGLSAIEVDRVARATGFTPGRVVTEALNRGGVAYAECALAAIAVLGHGPERPLTSDGRNREKARKFLALAHQRVRRQREWFLHNESAHYARTYSKIAIEDWSTKEMTASEPQGEETRRVTRSRNRSILDVGWYELGRQLAYKTEATGAEFAQVDPGLKETETNVPKAIADARDVDVSGMLRGEAGISGTCSKCGGLLRAPASGHADAECEICLNVEVGDVNAAVNVLKRAMFPGDAPPASGEKPKVSIGIKGRQKKKKAA 96MEAIATGMSPERRVELGILPGSVELKRAYKFRLYPMKVQQAELSEWERQLRRLYNLAHEQRLAALLRYRDWDFQKGACPSCRVAVPGVHTAACDHVDYFRQAREMTQLLEVDAQLS RVICCARQEVLRDLDKAWQRWRKKLGGRPRFKRRTDSCRIYLSTPKHWEIAGRYLRLSGLASSVGEIRIEQDRAFPEGALLSSCSIVRDVDEWYACLPLTFTQPIERAPHRSVGLNRGVVHALADSDGRVVDSPKFFERALATVQKRSRDLARKVSGSRNAHKARIKLAKAHQRVRRQRAAFLHQESAYYSKGFDLVALEDMSVRKMTATAGEAPEMGRGAQRDLNRGILDVGWYELARQIDYKRLAHGGELLRVDPGQTTPLACVTEEQPARGISSACAVCGIPLARPASGNARMRCTACGSSQVGDVNAAENVLTRALSSAPSGPKSPKASIKIKGRQKRLGTPANRAGEAS GGDPPVRGPVEGGTLAYVVEPVSESQSDT 97MTVRTYKYRAYPTPEQAEALTSWLRFASQLYNAALEHRKNAWGRHDAHGRGFRFWDGDAAPRKKSDPPGRWVYRGGGGAHISKNDQGKLLTEFRREHAELLPPGMPALVQHEVLARLERSMAAFFQRATKGQKAGYPRWRSEHRYDSLTFGLTSPSKERFDPETGESLGRGKTVGAGTYHNGDLRLTGLGELRILEHRRIPMGAIPKSVIVRRSGKRWFVSIAMEMPSVEPAASGRPAVGLDMGVVTWGTAFTADTSAAAALVADLRRMATDPSDCRRLEELEREAAQLSEVLAHCRARGLDPARPRRCPKELTKLYRRSLHRLGELDRACARIRRRLQAAHDIAEPVPDEAGSAVLIEGSNAGMRHARRVARTQRRVARRTRAGHAHSNRRKKAVQAYARAKERERSARGDHRHKVSRALVRQFEEISVEALDIKQLTVAPEHNPDPQPDLPAHVQRRRNRGELDAAWGAFFAALDYKAADAGGRVARKPAPHTTQECARCGTLVPKPISLRVHRCPACGYTAPRTVNSARNVLQRPLEEPGRAGPSGANGRGVPHAVA 98MNCRYRYRIYPTPGQRQSLARLFGCVRVVWNDALFLCRQSEKLPKNSELQKLCITQAKK TEARGWLGQVSAIPLQQSVADLGVAFKNFFQSRSGKRKGKKVNPPRVKRRNNRQGARFTRGGFKVKTSKVYLARIGDIKIKWSRPLPSEPSSVTVIKDCAGQYFLSFVVEVKPEIKPPK NPSIGIDLGLKTFASCSNGEKIDSPDYSRLYRKLKRCQRRLAKRQRGSKRRERMRVKVAKLNAQIRDKRKDFLHKLSTKVVNENQVIALEDLNVGGMLKNRKLSRAISQAGWYEFRS LCEGKAEKHNRDFRVISRWEPTSQVCSECGYRWGKIDLSVRSIVCINCGVEHDRDDNAS VNIEQAGLKVGVGHTHDSKRTGSACKTSNGAVCVEPSTHREYVQLTLFDW 99MKSRWTFRCYPTPEQEQHLARTFGCVRFVWNWALRARTDAFRAGERIGYPATDKALTLLKQQPETVWLNEVSSVCLQQALRDLQVAFSNFFDKRAAHPSFKRKEARQSANYTERGFS FDHERRILKLAKIGAIKVKWSRKAIPHPSSIRLIRTASGKYFVSLVVETQPAPMPETGESVGVDFGVARLATLSNGERISNPKHGAKWQRRLAFYQKRLARATKGSKRRMRIKRHVARIHEKIGNSRSDTLHKLSTDLVTRFDLICVEDLNLRGMVKNHSLARSLHDASIGSAIRMIEEKAERYGKNVVKIDRWFPSSKTCSDCGHIVEQLPLNVREWTCPECGTTHDRDANAAANILAVGQTVSAHGGTVRRSRAKASERKSQRSANRQGVNRA 100KEPLNIGKTAKAVFKEIDPTSLNRAANYDASIELNCKECKFKPFKNVKRYEFNFYNNWYRCNPNSCLQSTYKAQVRKVEIGYEKLKNEILTQMQYYPWFGRLYQNFFHDERDKMTSLDEIQVIGVQNKVFFNTVEKAWREIIKKRFKDNKETMETIPELKHAAGHGKRKLSNKSLLRRRFAFVQKSFKFVDNSDVSYRSFSNNIACVLPSRIGVDLGGVISRNPKREYIPQEISFNAFWKQHEGLKKGRNIEIQSVQYKGETVKRIEADTGEDKAWGKNRQRRFTSLILKLVPKQGGKKVWKYPEKRNEGNYEYFPIPIEFILDSGETSIRFGGDEGEAGKQKHLVIPFNDSKATPLASQQTLLENSRFNAEVKSCIGLAIYANYFYGYARNYVISSIYHKNSKNGQAITAIYLESIAHNYVKAIERQLQNLLLNLRDFSFMESHKKELKKYFGGDLEGTGGAQKRREKEEKIEKEIEQSYLPRLIRLSLTKMVTKQVEM 101ELIVNENKDPLNIGKTAKAVFKEIDPTSINRAANYDASIELACKECKFKPFNNTKRHDFSFYSNWHRCSPNSCLQSTYRAKIRKTEIGYEKLKNEILNQMQYYPWFGRLYQNFFNDQRDK MTSLDEIQVTGVQNKIFFNTVEKAWREIIKKRFRDNKETMRTIPDLKNKSGHGSRKLSNK SLLRRRFAFAQKSFKLVDNSDVSYRAFSNNVACVLPSKIGVDIGGIINKDLKREYIPQEITFNVFWKQHDGLKKGRNIEIHSVQYKGEIVKRIEADTGEDKAWGKNRQRRFTSLILKITPK QGGKKIWKFPEKKNASDYEYFPIPIEFILDNGDASIKFGGEEGEVGKQKHLLIPFNDSKATPLSSKQMLLETSRFNAEVKSTIGLALYANYFVSYARNYVIKSTYHKNSKKGQIVTEIYLES ISQNFVRAIQRQLQSLMLNLKDWGFMQTHKKELKKYFGSDLEGSKGGQKRREKEEKIEK EIEASYLPRLIRLSLTKSVTKAEEM 102PEEKTSKLKPNSINLAANYDANEKFNCKECKFHPFKNKKRYEFNFYNNLHGCKSCTKSTNNPAVKRIEIGYQKLKFEIKNQMEAYPWFGRLRINFYSDEKRKMSELNEMQVTGVKNKIFFDAIECAWREILKKRFRESKETLITIPKLKNKAGHGARKHRNKKLLIRRRAFMKKNFHFLDNDSISYRSFANNIACVLPSKVGVDIGGIISPDVGKDIKPVDISLNLMWASKEGIKSGRK VEIYSTQYDGNMVKKIEAETGEDKSWGKNRKRRQTSLLLSIPKPSKQVQEFDFKEWPRYKDIEKKVQWRGFPIKIIFDSNHNSIEFGTYQGGKQKVLPIPFNDSKTTPLGSKMNKLEKLRFNSKIKSRLGSAIAANKFLEAARTYCVDSLYHEVSSANAIGKGKIFIEYYLEILSQNYIEAAQKQLQRFIESIEQWFVADPFQGRLKQYFKDDLKRAKCFLCANREVQTTCYAAVKLHKSCAEKVKDKNKELAIKERNNKEDAVIKEVEASNYPRVIRLKLTKTITNKAM 103SESENKIIEQYYAFLYSFRDKYEKPEFKNRGDIKRKLQNKWEDFLKEQNLKNDKKLSNYIFSNRNFRRSYDREEENEEGIDEKKSKPKRINCFEKEKNLKDQYDKDAINASANKDGAQK WGCFECIFFPMYKIESGDPNKRIIINKTRFKLFDFYLNLKGCKSCLRSTYHPYRSNVYIESNYDKLKREIGNFLQQKNIFQRMRKAKVSEGKYLTNLDEYRLSCVAMHFKNRWLFFDSIQKVLRETIKQRLKQMRESYDEQAKTKRSKGHGRAKYEDQVRMIRRRAYSAQAHKLLDNGYITLFDYDDKEINKVCLTAINQEGFDIGGYLNSDIDNVMPPIEISFHLKWKYNEPILNIES PFSKAKISDYLRKIREDLNLERGKEGKARSKKNVRRKVLASKGEDGYKKIFTDFFSKWK EELEGNAMERVLSQSSGDIQWSKKKRIHYTTLVLNINLLDKKGVGNLKYYEIAEKTKILS FDKNENKFWPITIQVUDGYEIGTEYDEIKQLNEKTSKQFTIYDPNTKIIKIPFTDSKAVPLGMLGINIATLKTVKKTERDIKVSKIFKGGLNSKIVSKIGKGIYAGYFPTVDKEILEEVEEDTLDNEFSSKSQRNIFLKSIIKNYDKMLKEQLFDFYSFLVRNDLGVRFLTDRELQNIEDESFNLEKRFFETDRDRIARWFDNTNTDDGKEKFKKLANEIVDSYKPRLIRLPVVRVIKRIQPVK  QREM 104KYSTRDFSELNEIQVTACKQDEFFKVIQNAWREIIKKRFLENRENFIEKKIFKNKKGRGKRQESDKTIQRNRASVMKNFQLIENEKIILRAPSGHVACVFPVKVGLDIGGFKTDDLEKNIFPPRTITINVFWKNRDRQRKGRKLEVWGIKARTKLIEKVHKWDKLEEVKKKRLKSLEQKQEKSLDNWSEVNNDSFYKVQIDELQEKIDKSLKGRTMNKILDNKAKESKEAEGLYIEWEK DFEGEMLRRIEASTGGEEKWGKRRQRRHTSULDIKNNSRGSKEIINFYSYAKQGKKEKK IEFFPFPLTITLDAEEESPLNIKSIPIEDKNATSKYFSIPFTETRATPLSILGDRVQKFKTKNISGAIKRNLGSSISSCKIVQNAETSAKSILSLPNVKEDNNMEIFINTMSKNYFRAMMKQMES FIFEMEPKTLIDPYKEKAIKWFEVAASSRAKRKLKKLSKADIKKSELLLSNTEEFEKEKQEKLEALEKEIEEFYLPRIVRLQLTKTILETPVM 105KKLQLLGHKILLKEYDPNAVNAAANFETSTAELCGQCKMKPFKNKRRFQYTFGKNYHGCLSCIQNVYYAKKRIVQIAKEELKHQLTDSIASIPYKYTSLFSNTNSIDELYILKQERAAFFSNTNSIDELYITGIENNIAFKVISAIWDEIIKKRRQRYAESLTDTGTVKANRGHGGTAYKS NTRQEKIRALQKQTLHMVTNPYISLARYKNNYIVATLPRTIGMHIGAIKDRDPQKKLSDYAINFNVFWSDDRQLIELSTVQYTGDMVRKIEAETGENNKWGENMKRTKTSLLLEILTKK TTDELTFKDWAFSTKKEIDSVTKKTYQGFPIGIIFEGNESSVKFGSQNYFPLPFDAKITPPTAEGFRLDWLRKGSFSSQMKTSYGLAIYSNKVTNAIPAYVIKNMFYKIARAENGKQIKAK FLKKYLDIAGNNYVPFIIMQHYRVLDTFEEMPISQPKVIRLSLTKTQHIIIKKDKTDSKM 106NTSNLINLGKKAINISANYDANLEVGCKNCKFLSSNGNFPRQTNVKEGCHSCEKSTYEPSIYLVKIGERKAKYDVLDSLKKFTFQSLKYQSKKSMKSRNKKPKELKEFVIFANKNKAFDVIQKSYNHLILQIKKEINRMNSKKRKKNHKRRLFRDREKQLNKLRLIESSNLFLPRENKGNNHVFTYVAIHSVGRDIGVIGSYDEKLNFETELTYQLYFNDDKRLLYAYKPKQNKIIKIKEKLWNLRKEKEPLDLEYEKPLNKSITFSIKNDNLFKVSKDLMLRRAKFNIQGKEKLSKEERKINRDLIKIKGLVNSMSYGRFDELKKEKNIWSPHIYREVRQKEIKPCLIKNGDRIEIFEQLK KKMERLRRFREKRQKKISKDLIFAERIAYNFHTKSIKNTSNKINIDQEAKRGKASYMRKRIGYETFKNKYCEQCLSKGNVYRNVQKGCSCFENPFDWIKKGDENLLPKKNEDLRVKGAFRDEALEKQIVKIAFNIAKGYEDFYDNLGESTEKDLKLKFKVGTTINEQESLKL 107TSNPIKLGKKAINISANYDSNLQIGCKNCKFLSYNGNFPRQTNVKEGCHSCEKSTYEPPVYTVRIGERRSKYDVLDSLKKFIFLSLKYRQSKKMKTRSKGIRGLEEFVISANLKKAMDVIQKSYRHLILNIKNEIVRMNGKKRNKNHKRLLFRDREKQLNKLRLIEGSSFFKPPTVKGDNSIFTCVAIHNIGRDIGIAGDYFDKLEPKIELTYQLYYEYNPKKESEINKRLLYAYKPKQNKIIEIKEKLWNLRKEKSPLDLEYEKPLTKSITFLVKRDGVFRISKDLMLRKAKFIIQGKEKLS KEERKINRDLIKIKSNIISLTYGRFDELKKDKTIWSPHIFRDVKQGKITPCIERKGDRMDIFQQLRKKSERLRENRKKRQKKISKDLIFAERIAYNFHTKSIKNTSNLINIKHEAKRGKASYMRKRIGNETFRIKYCEQCFPKNNVYKNVQKGCSCFEDPFEYIKKGNEDLIPNKNQDLKAKGAFRDDALEKQIIKVAFNIAKGYEDFYENLKKTTEKDIRLKFKVGTIISEEM 108NNSINLSKKAINISANYDANLQVRCKNCKFLSSNGNFPRQTDVKEGCHSCEKSTYEPPVYDVKIGEIKAKYEVLDSLKKFTFQSLKYQLSKSMKFRSKKIKELKEFVIFAKESKALNVINRSYKHLILNIKNDINRMNSKKRIKNHKGRLFLDRQKQLSKLKLIEGSSFFVPAKNVGNKSVFTCVAIHSIGRDIGIAGLYDSFTKPVNEITYQIFFSGERRLLYAYKPKQLKILSIKENLWSLKNEKKPLDLLYEKPLGKNLNFNVKGGDLFRVSKDLMIRNAKFNVHGRQRLSDEERLINRNFIKIKGEVVSLSYGRFEELKKDRKLWSPHIFKDVRQNKIKPCLVMQGQRIDIFEQLKRKLELLKKIRKSRQKKLSKDLIFGERIAYNFHTKSIKNTSNKINIDSDAKRGRASYMRKRIGNETFKLKYCDVCFPKANVYRRVQNGCSCSENPYNYIKKGDKDLLPKKDEGLAIKGAFRDEK LNKQIIKVAFNIAKGYEDFYDDLKKRTEKDVDLKFKIGTTVLDQKPMEIFDGIVITWL 109LLTTVVETNNLAKKAINVAANFDANIDRQYYRCTPNLCRFIAQSPRETKEKDAGCSSCTQSTYDPKVYVIKIGKLLAKYEILKSLKRFLFMNRYFKQKKTERAQQKQKIGTELNEMSIFAKATNAMEVIKRATKHCTYDIIPETKSLQMLKRRRHRVKVRSLLKILKERRMKIKKIPNTFIEIPKQAKKNKSDYYVAAALKSCGIDVGLCGAYEKNAEVEAEYTYQLYYEYKGNSSTKRILYCYNNPQKNIREFWEAFYIQGSKSHVNTPGTIRLKMEKFLSPITIESEALDFRVWNSDLKIRNGQYGFIKKRSLGKEAREIKKGMGDIKRKIGNLTYGKSPSELKSIHVYRTERENPKKPRAARKKEDNFMEIFEMQRKKDYEVNKKRRKEATDAAKIMDFAEEPIRHYHTNNLKAVRRIDMNEQVERKKTSVFLKRIMQNGYRGNYCRKCIKAPEGSNRDENVLEKNEGCLDCIGS EFIWKKSSKEKKGLWHTNRLLRRIRLQCFTTAKAYENFYNDLFEKKESSLDIIKLKVSITT KSM 110ASTMNLAKQAINFAANYDSNLEIGCKGCKFMSTWSKKSNPKFYPRQNNQANKCHSCTYSTGEPEVPIIEIGERAAKYKIFTALKKFVFMSVAYKERRRQRFKSKKPKELKELAICSNREKAMEVIQKSVVHCYGDVKQEIPRIRKIKVLKNHKGRLFYKQKRSKIKIAKLEKGSFFKTFIPKVHNNGCHSCHEASLNKPILVTTALNTIGADIGLINDYSTIAPTETDISWQVYYEFIPNGDSEAVKKRLLYFYKPKGALIKSIRDKYFKKGHENAVNTGFFKYQGKIVKGPIKFVNNELDFARKPDLKSMKIKRAGFAIPSAKRLSKEDREINRESIKIKNKIYSLSYGRKKTLSDKDIIK FILYRPVRQKGVKPLEYRKAPDGFLEFFYSLKRKERRLRKQKEKRQKDMSEIIDAADEFAWHRHTGSIKKTTNHINFKSEVKRGKVPIMKKRIANDSFNTRHCGKCVKQGNAINKYYIEKQKNCFDCNSIEFKWEKAALEKKGAFKLNKRLQYIVKACFNVAKAYESFYEDFRKGEEESLDLKFKIGTTTTLKQYPQNKARAM 111HSHNLMLTKLGKQAINFAANYDANLEIGCKNCKFLSYSPKQANPKKYPRQTDVHEDGNIACHSCMQSTKEPPVYIVPIGERKSKYEILTSLNKFTFLALKYKEKKRQAFRAKKPKELQELAIAFNKEKAIKVIDKSIQHLILNIKPEIARIQRQKRLKNRKGKLLYLHKRYAIKMGLIKNGKYFKVGSPKKDGKKLLVLCALNTIGRDIGIIGNIEENNRSETEITYQLYFDCLDANPNELRIKEIEYNRLKSYERKIKRLVYAYKPKQTKILEIRSKFFSKGHENKVNTGSFNFENPLNKSISIKVKNSAFDFKIGAPFIMLRNGKFHIPTKKRLSKEEREINRTLSKIKGRVFRLTYGRNISEQGSKSLHIYRKERQHPKLSLEIRKQPDSFIDEFEKLRLKQNFISKLKKQRQKKLADLLQFADRIAYNYHTSSLEKTSNFINYKPEVKRGRTSYIKKRIGNEGFEKLYCETCIKSNDKENAYAVEKEELCFVCKAKPFTWKKTNKDKLGIFKYPSRIKDFIRAAFTVAKSYNDFYENLKKKDLK NEIFLKFKIGLILSHEKKNHISIAKSVAEDERISGKSIKNILNKSIKLEKNCYSCFFHKEDM 112SLERVIDKRNLAKKAINIAANFDANINKGFYRCETNQCMFIAQKPRKTNNTGCSSCLQSTYDPVIYVVKVGEMLAKYEILKSLKRFVFMNRSFKQKKTEKAKQKERIGGELNEMSIFANAALAMGVIKRAIRHCHVDIRPEINRLSELKKTKHRVAAKSLVKIVKQRKTKWKGIPNSFIQIPQKARNKDADFYVASALKSGGIDIGLCGTYDKKPHADPRWTYQLYFDTEDESEKRLLYCYNDPQAKIRDFWKTFYERGNPSMVNSPGTIEFRMEGFFEKMTPISIESKDFDFRVWNK DLLIRRGLYEIKKRKNLNRKAREIKKAMGSVKRVLANMTYGKSPTDKKSIPVYRVEREK PKKPRAVRKEENELADKLENYRREDFLIRNRRKREATEIAKIIDAAEPPIRHYHTNHLRAVKRIDLSKPVARKNTSVFLKRIMQNGYRGNYCKKCIKGNIDPNKDECRLEDIKKCICCEGTQNIWAKKEKLYTGRINVLNKRIKQMKLECFNVAKAYENFYDNLAALKEGDLKVLKLKVSIPALNPEASDPEEDM 113NASINLGKRAINLSANYDSNLVIGCKNCKFLSFNGNFPRQTNVREGCHSCDKSTYAPEVYIVKIGERKAKYDVLDSLKKFTFQSLKYQIKKSMRERSKKPKELLEFVIFANKDKAFNVIQKSYEHLILNIKQEINRMNGKKRIKNHKKRLFKDREKQLNKLRLIGSSSLFFPRENKGDKDLFTYVAIHSVGRDIGVAGSYESHIEPISDLTYQLFINNEKRLLYAYKPKQNKIIELKENLWNLKKEKKPLDLEFTKPLEKSITFSVKNDKLFKVSKDLMLRQAKFNIQGKEKLSKEERQINRDFSKIKSNVISLSYGRFEELKKEKNIWSPHIYREVKQKEIKPCIVRKGDRIELFEQLKRKMDKLKKFRKERQKKISKDLNFAERIAYNFHTKSIKNTSNKINIDQEAKRGKASYMRKRIGNESFRKKYCEQCFSVGNVYHNVQNGCSCFDNPIELIKKGDEGLIPKGKEDRKYKGALRDDNLQMQIIRVAFNIAKGYEDFYNNLKEKTEKDLKLKFKIGTTISTQESNNKEM 114SNLIKLGKQAINFAANYDANLEVGCKNCKFLSSTNKYPRQTNVHLDNKMACRSCNQSTMEPAIYIVRIGEKKAKYDIYNSLTKFNFQSLKYKAKRSQRFKPKQPKELQELSIAVRKEK ALDIIQKSIDHLIQDIRPEIPRIKQQKRYKNHVGKLFYLQKRRKNKLNLIGKGSFFKVFSPK EKKNELLVICALTNIGRDIGLIGNYNTIINPLFEVTYQLYYDYIPKKNNKNVQRRLLYAYK SKNEKILKLKEAFFKRGHENAVNLGSFSYEKPLEKSLTLKIKNDKDDFQVSPSLRIRTGRFFVPSKRNLSRQEREINRRLVKIKSKIKNMTYGKFETARDKQSVHIFRLERQKEKLPLQFRK DEKEFMEEFQKLKRRTNSLKKLRKSRQKKLADLLQLSEKVVYNNHTGTLKKTSNFLNFS SSVKRGKTAYIKELLGQEGFETLYCSNCINKGQKTRYNIETKEKCFSCKDVPFVWKKKSTDKDRKGAFLFPAKLKDVIKATFTVAKAYEDFYDNLKSIDEKKPYIKFKIGLILAHVRHEHKARAKEEAGQKNIYNKPIKIDKNCKECFFFKEEAM 115NTTRKKFRKRTGFPQSDNIKLAYCSAIVRAANLDADIQKKHNQCNPNLCVGIKSNEQSRKYEHSDRQALLCYACNQSTGAPKVDYIQIGEIGAKYKILQMVNAYDFLSLAYNLTKLRNGKSRGHQRMSQLDEVVIVADYEKATEVIKRSINHLLDDIRGQLSKLKKRTQNEHITEHKQSKIRRKLRKLSRLLKRRRWKWGTIPNPYLKNWVFTKKDPELVTVALLHKLGRDIGLVNRSKRRSKQKLLPKVGFQLYYKWESPSLNNIKKSKAKKLPKRLLIPYKNVKLFDNKQKLENAIKSLLESYQKTIKVEFDQFFQNRTEEIIAEEQQTLERGLLKQLEKKKNEFASQKKALKEEKKKIKEPRKAKLLMEESRSLGFLMANVSYALFNTTIEDLYKKSNVVSGCIPQEPVVVFPADIQNKGSLAKILFAPKDGFRIKFSGQHLTIRTAKFKIRGKEIKILTKTKREILKNIEKLRRVWYREQHYKLKLFGKEVSAKPRFLDKRKTS IERRDPNKLADQTDDRQAELRNKEYELRHKQHKMAERLDNIDTNAQNLQTLSFWVGEADKPPKLDEKDARGFGVRTCISAWKWFMEDLLKKQEEDPLLKLKLSIM 116PKKPKFQKRTGFPQPDNLRKEYCLAIVRAANLDADFEKKCTKCEGIKTNKKGNIVKGRTYNSADKDNLLCYACNISTGAPAVDYVFVGALEAKYKILQMVKAYDFHSLAYNLAKLWKGRGRGHQRMGGLNEVVIVSNNEKALDVIEKSLNHFHDEIRGELSRLKAKFQNEHLHVHKESKLRRKLRKISRLLKRRRWKWDVIPNSYLRNFTFTKTRPDFISVALLHRVGRDIGLVTKTKIPKPTDLLPQFGFQIYYTWDEPKLNKLKKSRLRSEPKRLLVPYKKIELYKNKSVLEEAIRHLAEVYTEDLTICFKDFFETQKRKFVSKEKESLKRELLKELTKLKKDFSERKTALKRDRKEIKEPKKAKLLMEESRSLGFLAANTSYALFNLIAADLYTKSKKACSTKLPRQLSTILPLEIKEHKSTTSLAIKPEEGFKIRFSNTHLSIRTPKFKMKGADIKALTKRKREILKNATKLEK SWYGLKHYKLKLYGKEVAAKPRFLDKRNPSIDRRDPKELMEQIENRRNEVKDLEYEIRK GQHQMAKRLDNVDTNAQNLQTKSFWVGEADKPPELDSMEAKKLGLRTCISAWKWFMKDLVLLQEKSPNLKLKLSLTEM 117KFSKRQEGFLIPDNIDLYKCLAIVRSANLDADVQGHKSCYGVKKNGTYRVKQNGKKGVKEKGRKYVFDLIAFKGNIEKIPHEAIEEKDQGRVIVLGKFNYKLILNIEKNHNDRASLEIK NKIKKLVQISSLETGEFLSDLLSGKIGIDEVYGIIEPDVFSGKELVCKACQQSTYAPLVEYMPVGELDAKYKILSAIKGYDFLSLAYNLSRNRANKKRGHQKLGGGELSEVVISANYDKALNVIKRSINHYHVEIKPEISKLKKKMQNEPLKVMKQARIRRELHQLSRKVKRLKWKWGMIPNPELQNIIFEKKEKDFVSYALLHTLGRDIGLFKDTSMLQVPNISDYGFQIYYSWEDPKLNSIKKIKDLPKRLLIPYKRLDFYIDTILVAKVIKNLIELYRKSYVYETFGEEYGYAKKAEDILFDWDSINLSEGIEQKIQKIKDEFSDLLYEARESKRQNFVESFENILGLYDKNFASDRNSYQEKIQSMIIKKQQENIEQKLKREFKEVIERGFEGMDQNKKYYKVLSPNIKGGLLYTDTNNLGFFRSHLAFMLLSKISDDLYRKNNLVSKGGNKGILDQTPETMLTLEFGKSNLPNISIKRKFFNIKYNSSWIGIRKPKFSIKGAVIREITKKVRDEQRLIKSLEGVWHKSTHFKRWGKPRFNLPRHPDREKNNDDNLMESITSRREQIQLLLREKQKQQEKMAGRLDKIDKEIQNLQTANFQIKQIDKKPALTEKSEGKQSVRNALSAWKWFMEDLIKYQKRTPILQLKLAKM 118KFSKRQEGFVIPENIGLYKCLAIVRSANLDADVQGHVSCYGVKKNGTYVLKQNGKKSIREKGRKYASDLVAFKGDIEKIPFEVIEEKKKEQSIVLGKFNYKLVLDVMKGEKDRASLTMKNKSKKLVQVSSLGTDEFLLTLLNEKFGIEEIYGIIEPEVFSGKKLVCKACQQSTYAPLVEYMPVGELDSKYKILSAIKGYDFLSLAYNLARHRSNKKRGHQKLGGGELSEVVISANNAK ALNVIKRSLNHYYSEIKPEISKLRKKMQNEPLKVGKQARMRRELHQLSRKVKRLKWKWGKIPNLELQNITFKESDRDFISYALLHTLGRDIGMFNKTEIKMPSNILGYGFQIYYDWEEPKLNTIKKSKNTPKRILIPYKKLDFYNDSILVARAIKELVGLFQESYEWEIFGNEYNYAKEAEVELIKLDEESINGNVEKKLQRIKENFSNLLEKAREKKRQNFIESFESIARLYDESFTADRNEYQREIQSFIIEKQKQSIEKKLKNEFKKIVEKKFNEQEQGKKHYRVLNPTIINEFLPKDKNNLGFLRSKIAFILLSKISDDLYKKSNAVSKGGEKGIIKQQPETILDLEFSKSKLPSINIKKKLFNIKYTSSWLGIRKPKFNIKGAKIREITRRVRDVQRTLKSAESSWYASTHFRRWGFPRFNQPRHPDKEKKSDDRLIESITLLREQIQILLREKQKGQKEMAGRLDDVDKKIQNLQTANFQIKQTGDKPALTEKSAGKQSFRNALSAWKWFMENLLKYQNKTPDLKLKIARTVM 119KWIEPNNIDFNKCLAITRSANLDADVQGHKMCYGIKTNGTYKAIGKINKKHNTGIIEKRRTYVYDLIVTKEKNEKIVKKTDFMAIDEEIEFDEKKEKLLKKYIKAEVLGTGELIRKDLNDGEKFDDLCSIEEPQAFRRSELVCKACNQSTYASDIRYIPIGEIEAKYKILKAIKGYDFLSLK YNLGRLRDSKKRGHQKMGQGELKEFVICANKEKALDVIKRSLNHYLNEVKDEISRLNK KMQNEPLKVNDQARWRRELNQISRRLKRLKWKWGEIPNPELKNLIFKSSRPEFVSYALIHTLGRDIGLINETELKPNNIQEYGFQIYYKWEDPELNHIKKVKNIPKRFIIPYKNLDLFGKYTILSRAIEGILKLYSSSFQYKSFKDPNLFAKEGEKKITNEDFELGYDEKIKKIKDDFKSYKK ALLEKKKNTLEDSLNSILSVYEQSLLTEQINNVKKWKEGLLKSKESIHKQKKIENIEDIISRIEELKNVEGWIRTKERDIVNKEETNLKREIKKELKDSYYEEVRKDFSDLKKGEESEKKPFREEPKPIVIKDYIKFDVLPGENSALGFFLSHLSFNLFDSIQYELFEKSRLSSSKHPQIPETI LDL 120FRKFVKRSGAPQPDNLNKYKCIAIVRAANLDADIMSNESSNCVMCKGIKMNKRKTAKGAAKTTELGRVYAGQSGNLLCTACTKSTMGPLVDYVPIGRIRAKYTILRAVKEYDFLSLAYNLARTRVSKKGGRQKMHSLSELVIAAEYEIAWNIIKSSVIHYHQETKEEISGLRKKLQAEHIHKNKEARIRREMHQISRRIKRLKWKWHMIPNSELHNFLFKQQDPSFVAVALLHTLGRDIGMINKPKGSAKREFIPEYGFQIYYKWMNPKLNDINKQKYRKMPKRSLIPYKNLNVFGDRELIENAMHKLLKLYDENLEVKGSKFFKTRVVAISSKESEKLKRDLLWKGELAKIKK DFNADKNKMQELFKEVKEPKKANALMKQSRNMGFLLQNISYGALGLLANRMYEASAK QSKGDATKQPSIVIPLEMEFGNAFPKLLLRSGKFAMNVSSPWLTIRKPKFVIKGNKIKNITKLMKDEKAKLKRLETSYHRATHFRPTLRGSIDWDSPYFSSPKQPNTHRRSPDRLSADITEYRGRLKSVEAELREGQRAMAKKLDSVDMTASNLQTSNFQLEKGEDPRLTEIDEKGRSIRNCISSWKKFMEDLMKAQEANPVIKIKIALKDESSVLSEDSM 121KFHPENLNKSYCLAIVRAANLDADIQGHINCIGIKSNKSDRNYENKLESLQNVELLCKACTKSTYKPNINSVPVGEKKAKYSILSEIKKYDFNSLVYNLKKYRKGKSRGHQKLNELRELVITSEYKKALDVINKSVNHYLVNIKNKMSKLKKILQNEHIHVGTLARIRRERNRISRKLDHYRKKWKFVPNKILKNYVFKNQSPDFVSVALLHKLGRDIGLITKTAILQKSFPEYSLQLYYKYDTPKLNYLKKSKFKSLPKRILISYKYPKFDINSNYIEESIDKLLKLYEESPIYKNNSKIIEFFKKSEDNLIKSENDSLKRGIMKEFEKVTKNFSSKKKKLKEELKLKNEDKNSKMLAKVSRPIGFLKAYLSYMLFNIISNRIFEFSRKSSGRIPQLPSCIINLGNQFENFKNELQDSNIGSKKNYKYFCNLLLKSSGFNISYEEEHLSIKTPNFFINGRKLKEITSEKKKIRKENEQLIKQWKKLTFFKPSNLNGKKTSDKIRFKSPNNPDIERKSEDNIVENIAKVKYKLEDLLSEQRKEFNKLAK KHDGVDVEAQCLQTKSFWIDSNSPIKKSLEKKNEKVSVKKKMKAIRSCISAWKWFMADLIEAQKETPMIKLKLALM 122TTLVPSHLAGIEVMDETTSRNEDMIQKETSRSNEDENYLGVKNKCGINVHKSGRGSSKHEPNMPPEKSGEGQMPKQDSTEMQQRFDESVTGETQVSAGATASIKTDARANSGPRVGTARALIVKASNLDRDIKLGCKPCEYIRSELPMGKKNGCNHCEKSSDIASVPKVESGFRKAK YELVRRFESFAADSISRHLGKEQARTRGKRGKKDKKEQMGKVNLDEIAILKNESLIEYTENQILDARSNRIKEWLRSLRLRLRTRNKGLKKSKSIRRQLITLRRDYRKWIKPNPYRPDEDPNENSLRLHTKLGVDIGVQGGDNKRMNSDDYETSFSITWRDTATRKICFTKPKGLLPRHMKFKLRGYPELILYNEELRIQDSQKFPLVDWERIPIFKLRGVSLGKKKVKALNRITEAPRLVVAKRIQVNIESKKKKVLTRYVYNDKSINGRLVKAEDSNKDPLLEFKKQAEEINSDAKYYENQEIAKNYLWGCEGLHKNLLEEQTKNPYLAFKYGFLNIV 123LDFKRTCSQELVLLPEIEGLKLSGTQGVTSLAKKLINKAANVDRDESYGCHHCIHTRTSLSKPVKKDCNSCNQSTNHPAVPITLKGYKIAFYELWHRFTSWAVDSISKALHRNKVMGK VNLDEYAVVDNSHIVCYAVRKCYEKRQRSVRLHKRAYRCRAKHYNKSQPKVGRIYKK SKRRNARNLKKEAKRYFQPNEITNGSSDALFYKIGVDLGIAKGTPETEVKVDVSICFQVYYGDARRVLRVRKMDELQSFHLDYTGKLKLKGIGNKDTFTIAKRNESLKWGSTKYEVSRAHKKFKPFGKKGSVKRKCNDYFRSIASWSCEAASQRAQSNLKNAFPYQKALVKCYKNLDYKGVKKNDMWYRLCSNRIFRYSRIAEDIAQYQSDKGKAKFEFVILAQSVAEYDISAIM 124VFLTDDKRKTALRKIRSAFRKTAEIALVRAQEADSLDRQAKKLTIETVSFGAPGAKNAFIGSLQGYNWNSHRANVPSSGSAKDVFRITELGLGIPQSAHEASIGKSFELVGNVVRYTANLLSKGYKKGAVNKGAKQQREIKGKEQLSFDLISNGPISGDKLINGQKDALAWWLIDKMGFHIGLAMEPLSSPNTYGITLQAFWKRHTAPRRYSRGVIRQWQLPFGRQLAPLIHNFFRKKGASIPIVLTNASKKLAGKGVLLEQTALVDPKKWWQVKEQVTGPLSNIWERSVPLVLYTATFTHKHGAAHKRPLTLKVIRISSGSVFLLPLSKVTPGKLVRAWMPDINILRDGRPDEAAYK GPDLIRARERSFPLAYTCVTQIADEWQKRALESNRDSITPLEAKLVTGSDLLQIHSTVQQAVEQGIGGRISSPIQELLAKDALQLVLQQLFMTVDLLRIQWQLKQEVADGNTSEKAVGWAIRISNIHKDAYKTAIEPCTSALKQAWNPLSGFEERTFQLDASIVRKRSTAKTPDDELVIVLRQQAAEMTVAVTQSVSKELMELAVRHSATLHLLVGEVASKQLSRSADKDRGAMDHWKL LSQSM 125EDLLQKALNTATNVAAIERHSCISCLFTESEIDVKYKTPDKIGQNTAGCQSCTFRVGYSGNSHTLPMGNRIALDKLRETIQRYAWHSLLFNVPPAPTSKRVRAISELRVAAGRERLFTVITFVQTNILSKLQKRYAANWTPKSQERLSRLREEGQHILSLLESGSWQQKEVVREDQDLIVCSALTKPGLSIGAFCRPKYLKPAKHALVLRLIFVEQWPGQIWGQSKRTRRMRRRKDVERVYDISVQAWALKGKETRISECIDTMRRHQQAYIGVLPFLILSGSTVRGKGDCPILKEITRMRYCPNNEGLIPLGIFYRGSANKLLRVVKGSSFTLPMWQNIETLPHPEPFSPEGWTATGALYEKNLAYWSALNEAVDWYTGQILSSGLQYPNQNEFLARLQNVIDSIPRKWFRPQGLKNLK PNGQEDIVPNEFVIPQNAIRAHHVIEWYHKTNDLVAKTLLGWGSQTTLNQTRPQGDLRFTYTRYYFREKEVPEV 126VPKKKLMRELAKKAVFEAIFNDPIPGSFGCKRCTLIDGARVTDAIEKKQGAKRCAGCEPTFHTLYDSVKHALPAATGCDRTAIDTGLWEILTALRSYNWMSFRRNAVSDASQKQVWSIEELAIWADKERALRVILSALTHTIGKLKNGFSRDGVWKGGKQLYENLAQKDLAKGLFANGEIFGKELVEADHDMLAWTIVPNHQFHIGLIRGNWKPAAVEASTAFDARWLTNGAPLRDTRTHGHRGRRFNRTEKLTVLCIKRDGGVSEEFRQERDYELSVMLLQPKNKLKPEPKGELNSFEDLHDHWWFLKGDEATALVGLTSDPTVGDFIQLGLYIRNPIKAHGETKRRLLICFEPPIKLPLRRAFPSEAFKTWEPTINVFRNGRRDTEAYYDIDRARVFEFPETRVSLEHLSKQWEVLRLEPDRENTDPYEAQQNEGAELQVYSLLQEAAQKMAPKVVIDPFGQFPLELFSTFVAQLFNAPLSDTKAKIGKPLDSGFVVESHLHLLEEDFAYRDFVRVTFMGTEPTFRVIHYS NGEGYWKKTVLKGKNNIRTALIPEGAKAAVDAYKNKRCPLTLEAAILNEEKDRRLVLGNKALSLLAQTARGNLTILEALAAEVLRPLSGTEGVVHLHACVTRHSTLTESTETDNM 127VEKLFSERLKRAMWLKNEAGRAPPAETLTLKHKRVSGGHEKVKEELQRVLRSLSGTNQAAWNLGLSGGREPKSSDALKGEKSRVVLETVVFHSGHNRVLYDVIEREDQVHQRSSIMEIMRRKGSNLLRLWGRSGKVRRKMREEVAEIKPVWHKDSRWLAIVEEGRQSVVGISSAGLAVFAVQESQCTTAEPKPLEYVVSIWFRGSKALNPQDRYLEFKKLKTTEALRGQQYDPIPFSLKRGAGCSLAIRGEGIKFGSRGPIKQFFGSDRSRPSHADYDGKRRLSLFSKYAGDLADLTEEQWNRTVSAFAEDEVRRATLANIQDFLSISHEKYAERLKKRIESIEEPVSASKLEAYLS AIFETFVQQREALASNFLMRLVESVALLISLEEKSPRVEFRVARYLAESKEGFNRKAM 128VVITQSELYKERLLRVMEIKNDRGRKEPRESQGLVLRFTQVTGGQEKVKQKLWLIFEGFS GTNQASWNFGQPAGGRKPNSGDALKGPKSRVTYETVVFHFGLRLLSAVIERHNLKQQRQTMAYMKRRAAARKKWARSGKKCSRMRNEVEKIKPKWHKDPRWFDIVKEGEPSIVGIS SAGFAIYIVEEPNFPRQDPLEIEYAISIWFRRDRSQYLTFKKIQKAEKLKELQYNPIPFRLK QEKTSLVFESGDIKFGSRGSIEHFRDEARGKPPKADMDNNRRLTMFSVFSGNLTNLTEEQYARPVSGLLAPDEKRMPTLLKKLQDFFTPIHEKYGERIKQRLANSEASKRPFKKLEEYLPAIYLEFRARREGLASNWVLVLINSVRTLVRIKSEDPYIEFKVSQYLLEKEDNKAL 129KQDALFEERLKKAIFIKRQADPLQREELSLLPPNRKIVTGGHESAKDTLKQILRAINGTNQASWNPGTPSGKRDSKSADALAGPKSRVKLETVVFHVGHRLLKKVVEYQGHQKQQHGLKAFMRTCAAMRKKWKRSGKVVGELREQLANIQPKWHYDSRPLNLCFEGKPSVVGLRS AGIALYTIQKSVVPVKEPKPIEYAVSIWFRGPKAMDREDRCLEFKKLKIATELRKLQFEPIVSTLTQGIKGFSLYIQGNSVKFGSRGPIKYFSNESVRQRPPKADPDGNKRLALFSKFSGDLSDLTEEQWNRPILAFEGIIRRATLGNIQDYLTVGHEQFAISLEQLLSEKESVLQMSIEQQRLKKNLGKKAENEWVESFGAEQARKKAQGIREYISGFFQEYCSQREQWAENWVQQLNKS VRLFLTIQDSTPFIEFRVARYLPKGEKKKGKAM 130ANHAERHKRLRKEANRAANRNRPLVADCDTGDPLVGICRLLRRGDKMQPNKTGCRSCEQVEPELRDAILVSGPGRLDNYKYELFQRGRAMAVHRLLKRVPKLNRPKKAAGNDEKKAENKKSEIQKEKQKQRRMMPAVSMKQVSVADFKHVIENTVRHLFGDRRDREIAECAALRAASKYFLKSRRVRPRKLPKLANPDHGKELKGLRLREKRAKLKKEKEKQAELARSNQKGAVLHVATLKKDAPPMPYEKTQGRNDYTTFVISAAIKVGATRGTKPLLTPQPREWQCSLYWRDGQRWIRGGLLGLQAGIVLGPKLNRELLEAVLQRPIECRMSGCGNPLQVRGAAVDFFMTTNPFYVSGAAYAQKKFKPFGTKRASEDGAAAKAREKLMTQLAKVLDKVVTQAAHSPLDGIWETRPEAKLRAMIMALEHEWIFLRPGPCHNAAEEVIKCDCTGGHAILWALIDEARGALEHKEFYAVTRAHTHDCEKQKLGGRLAGFLDLLIAQDVPLDDAPAARKIKTLLEATPPAPCYKAATSIATCDCEGKFDKLWAIIDATRAGHGTEDLWARTLAYPQNVNCKCKAGKDLTHRLADFLGLLIKRDGPFRERPPHKVTGDRKLVFSGDKKCKGHQYVILAKAHNEEVVRAWISRWGLKSRTNKAGYAATELNLLLNWLSICRRRWMDMLTVQRDTPYIRMKTGR LVVDDKKERKAM131 AKQREALRVALERGIVRASNRTYTLVTNCTKGGPLPEQCRMIERGKARAMKWEPKLVGCGSCAAATVDLPAIEEYAQPGRLDVAKYKLTTQILAMATRRMMVRAAKLSRRKGQWPAKVQEEKEEPPEPKKMLKAVEMRPVAIVDFNRVIQTTIEHLWAERANADEAELKALKAAAAYFGPSLKIRARGPPKAAIGRELKKAHRKKAYAERKKARRKRAELARSQARGAAAHAAIRERDIPPMAYERTQGRNDVTTIPIAAAIKIAATRGARPLPAPKPMKWQCSLYWNEGQRWIRGGMLTAQAYAHAANIHRPMRCEMWGVGNPLKVRAFEGRVADPDGAKGRKAEFRLQTNAFYVSGAAYRNKKFKPFGTDRGGIGSARKKRERLMAQLAKILDKVVSQAAHSPLDDIWHTRPAQKLRAMIKQLEHEWMFLRPQAPTVEGTKPDVDVAGNMQRQIKALMAPDLPPIEKGSPAKRFTGDKRKKGERAVRVAEAHSDEVVTAWISRWGIQTRRNEGSYAAQELELLLNWLQICRRRWLDMTAAQRVSPYIRMKSGRMITDAADEGVAPIPLVENM 132KSISGRSIKHMACLKDMLKSEITEIEEKQKKESLRKWDYYSKFSDEILFRRNLNVSANHDANACYGCNPCAFLKEVYGFRIERRNNERIISYRRGLAGCKSCVQSTGYPPIEFVRRKFGADKAMEIVREVLHRRNWGALARNIGREKEADPILGELNELLLVDARPYFGNKSAANETNLAFNVITRAAKKFRDEGMYDIHKQLDIHSEEGKVPKGRKSRLIRIERKHKAIHGLDPGETWRYPHCGKGEKYGVWLNRSRLIHIKGNEYRCLTAFGTTGRRMSLDVACSVLGHPLVKKK RKKGKKTVDGTELWQIKKATETLPEDPIDCTFYLYAAKPTKDPFILKVGSLKAPRWKKLFIKDFFEYSDTEKTQGQEKGKRVVRRGKVPRILSLRPDAKFKVSIWDDPYNGKNKEGTLLRMELSGLDGAKKPLILKRYGEPNTKPKNFVFWRPHITPHPLTFTPKHDFGDPNKKTKRRRVFNREYYGHLNDLAKMEPNAKFFEDREVSNKKNPKAKNIRIQAKESLPNIVAKNGRWAAFDPNDSLWKLYLHWRGRRKTIKGGISQEFQEFKERLDLYKKHEDESEWKEKEKLWENHEKEWKKTLEIHGSIAEVSQRCVMQSMMGPLDGLVQKKDYVHIGQSSLKAADDAWTFS ANRYKKATGPKWGKISVSNLLYDANQANAELISQSISKYLSKQKDNQGCEGRKMKFLIK IIEPLRENFVKHTRWLHEMTQKDCEVRAQFSRVSM 133FPSDVGADALKHVRMLQPRLTDEVRKVALTRAPSDRPALARFAAVAQDGLAFVRHLNVSANHDSNCTFPRDPRDPRRGPCEPNPCAFLREVWGFRIVARGNERALSYRRGLAGCKSCVQSTGFPSVPFHRIGADDCMRKLHEILKARNWRLLARNIGREREADPLLTELSEYLLVDARTYPDGAAPNSGRLAENVIKRAAKKFRDEGMRDIHAQLRVHSREGKVPKGRLQRLRRIERKHRAIHALDPGPSWEAEGSARAEVQGVAVYRSQLLRVGEIHTQQIEPVGIVARTLFGVGRTDLDVAVSVLGAPLTKRKKGSKTLESTEDFRIAKARETRAEDKIEVAFVLYPTASLLRDEIPKDAFPAMRIDRFLLKVGSVQADREILLQDDYYRFGDAEVKAGKNKGRTVTRPVKVPRLQALRPDAKFRVNVWADPFGAGDSPGTLLRLEVSGVTRRSQPLRLLRYGQPSTQPANFLCWRPHRVPDPMTFTPRQKFGERRKNRRTRRPRVFERLYQVHIKHLAHLEPNRKWFEEARVSAQKWAKARAIRRKGAEDIPVVAPPAKRRWAALQPNAELWDLYAHDREARKRFRGGRAAEGEEFKPRLNLYLAHEPEAEWESKRDRWERYEKKWTAVLEEHSRMCAVADRTLPQFLSDPLGARMDDKDYAFVGKSALAVAEAFVEEGTVERAQGNCSITAKKKFASNASRKRLSVANLLDVSDKADRALVFQAVRQYVQRQAENGGVEGRRMAFLRKLLAPLRQNFV CHTRWLHM 134AARKKKRGKIGITVKAKEKSPPAAGPFMARKLVNVAANVDGVEVHLCVECEADAHGS ASARLLGGCRSCTGSIGAEGRLMGSVDVDRERVIAEPVHTETERLGPDVKAFEAGTAES KYAIQRGLEYWGVDLISRNRARTVRKMEEADRPESSTMEKTSWDEIAIKTYSQAYHASENHLFWERQRRVRQHALALFRRARERNRGESPLQSTQRPAPLVLAALHAEAAAISGRARAEYVLRGPSANVRAAAADIDAKPLGHYKTPSPKVARGFPVKRDLLRARHRIVGLSRAYFK PSDVVRGTSDAIAHVAGRNIGVAGGKPKEIEKTFTLPFVAYWEDVDRVVHCSSFKADGPWVRDQRIKIRGVSSAVGTFSLYGLDVAWSKPTSFYIRCSDIRKKFHPKGFGPMKHWRQWAKELDRLTEQRASCVVRALQDDEELLQTMERGQRYYDVFSCAATHATRGEADPSGGCS RCELVSCGVAHKVTKKAKGDTGIEAVAVAGCSLCESKLVGPSKPRVHRQMAALRQSHALNYLRRLQREWEALEAVQAPTPYLRFKYARHLEVRSM 135AAKKKKQRGKIGISVKPKEGSAPPADGPFMARKLVNVAANVDGVEVNLCIECEADAHGSAPARLLGGCKSCTGSIGAEGRLMGSVDVDRADAIAKPVNTETEKLGPDVQAFEAGTAETKYALQRGLEYWGVDLISRNRSRTVRRTEEGQPESATMEKTSWDEIAIKSYTRAYHASENHLFWERQRRVRQHALALFKRAKERNRGDSTLPREPGHGLVAIAALACEAYAVGGRNLAETVVRGPTFGTARAVRDVEIASLGRYKTPSPKVAHGSPVKRDFLRARHRIVGLARAYYRPSDVVRGTSDAIAHVAGRNIGVAGGKPRAVEAVFTLPFVAYWEDVDRVVHCSSFQVS APWNRDQRMKIAGVTTAAGTFSLHGGELKWAKPTSFYIRCSDTRRKFRPKGFGPMKRWRQWAKDLDRLVEQRASCVVRALQDDAALLETMERGQRYYDVFACAVTHATRGEADRLAGCSRCALTPCQEAHRVTTKPRGDAGVEQVQTSDCSLCEGKLVGPSKPRLHRTLTLLRQEHGLNYLRRLQREWESLEAVQVPTPYLRFKYARHLEVRSM 136TDSQSESVPEVVYALTGGEVPGRVPPDGGSAEGARNAPTGLRKQRGKIKISAKPSKPGSPASSLARTLVNEAANVDGVQSSGCATCRMRANGSAPRALPIGCVACASSIGRAPQEETVCALPTTQGPDVRLLEGGHALRKYDIQRALEYWGVDLIGRNLDRQAGRGMEPAEGATATMKRVSMDELAVLDFGKSYYASEQHLFAARQRRVRQHAKALKIRAKHANRSGSVKRALDRSRKQVTALAREFFKPSDVVRGDSDALAHVVGRNLGVSRHPAREIPQTFTLPLCAYWEDVDRVISCSSLLAGEPFARDQEIRIEGVSSALGSLRLYRGAIEWHKPTSLYIRCSDTRRKFRPRGGLKKRWRQWAKDLDRLVEQRACCIVRSLQADVELLQTMERAQRFYDVHDCAATHVGPVAVRCSPCAGKQFDWDRYRLLAALRQEHALNYLRRLQREWESLEAQQVKMPYLRFKYARKLEVSGPLIGLEVRREPSMGTAIAEM 137AGTAGRRHGSLGARRSINIAGVTDRHGRWGCESCVYTRDQAGNRARCAPCDQSTYAPDVQEVTIGQRQAKYTIFLTLQSFSWTNTMRNNKRAAAGRSKRTTGKRIGQLAEIKITGVGLAHAHNVIQRSLQHNITKMWRAEKGKSKRVARLKKAKQLTKRRAYFRRRMSRQSRGNGFFRTGKGGIHAVAPVKIGLDVGMIASGSSEPADEQTVTLDAIWKGRKKKIRLIGAKGELAVAACRFREQQTKGDKCIPLILQDGEVRWNQNNWQCHPKKLVPLCGLEVSRKFVSQADRLAQNKVASPLAARFDKTSVKGTLVESDFAAVLVNVTSIYQQCHAMLLRSQEPTPSLRVQ RTITSM 138GVRFSPAQSQVFFRTVIPQSVEARFAINMAAIHDAAGAFGCSVCRFEDRTPRNAKAVHGCSPCTRSTNRPDVFVLPVGAIKAKYDVFMRLLGFNWTHLNRRQAKRVTVRDRIGQLDELAISMLTGKAKAVLKKSICHNVDKSFKAMRGSLKKLHRKASKTGKSQLRAKLSDLRERTNTTQEGSHVEGDSDVALNKIGLDVGLVGKPDYPSEESVEVVVCLYFVGKVLILDAQGRIRDMRAKQYDGFKIPIIQRGQLTVLSVKDLGKWSLVRQDYVLAGDLRFEPKISKDRKYAECVKRIALITLQASLGFKERIPYYVTKQVEIKNASHIAFVTEAIQNCAENFREMTEYLMKYQEKSPDLKVLLTQLM 139RAVVGKVFLEQARRALNLATNFGTNHRTGCNGCYVTPGKLSIPQDGEKNAAGCTSCLMKATASYVSYPKPLGEKVAKYSTLDALKGFPWYSLRLNLRPNYRGKPINGVQEVAPVSKFRLAEEVIQAVQRYHFTELEQSFPGGRRRLRELRAFYTKEYRRAPEQRQHVVNGDRNIVVVTVLHELGFSVGMFNEVELLPKTPIECAVNVFIRGNRVLLEVRKPQFDKERLLVESLWKK DSRRHTAKWTPPNNEGRIFTAEGWKDFQLPLLLGSTSRSLRAIEKEGFVQLAPGRDPDYNNTIDEQHSGRPFLPLYLYLQGTISQEYCVFAGTWVIPFQDGISPYSTKDTFQPDLKRKAYS LLLDAVKHRLGNKVASGLQYGRFPAIEELKRLVRMHGATRKIPRGEKDLLKKGDPDTPEWWLLEQYPEFWRLCDAAAKRVSQNVGLLLSLKKQPLWQRRWLESRTRNEPLDNLPLS  MALTLHLTNEEAL140 AAVYSKFYIENHFKMGIPETLSRIRGPSIIQGFSVNENYINIAGVGDRDFIFGCKKCKYTRGKPSSKKINKCHPCKRSTYPEPVIDVRGSISEFKYKIYNKLKQEPNQSIKQNTKGRMNPSDHTSSNDGIIINGIDNRIAYNVIFSSYKHLMEKQINLLRDTTKRKARQIKKYNNSGKKKHSLRSQTKGNLKNRYHMLGMFKKGSLTITNEGDFITAVRKVGLDISLYKNESLNKQEVETELCLNIKWGRTKSYTVSGYIPLPINIDWKLYLFEKETGLTLRLFGNKYKIQSKKFLIAQLFKPK RPPCADPVVKKAQKWSALNAHVQQMAGLFSDSHLLKRELKNRMHKQLDFKSLWVGTEDYIKWFEELSRSYVEGAEKSLEFFRQDYFCFNYTKQTTM 141PQQQRDLMLMAANYDQDYGNGCGPCTVVASAAYRPDPQAQHGCKRHLRTLGASAVTHVGLGDRTATITALHRLRGPAALAARARAAQAASAPMTPDTDAPDDRRRLEAIDADDVVLVGAHRALWSAVRRWADDRRAALRRRLHSEREWLLKDQIRWAELYTLIEASGTPPQGRWRNTLGALRGQSRWRRVLAPTMRATCAETHAELWDALAELVPEMAKDRRGLLRPPVEADALWRAPMIVEGWRGGHSVVVDAVAPPLDLPQPCAWTAVRLSGDPRQRWGLHLAVPPLGQVQPPDPLKATLAVSMRHRGGVRVRTLQAMAVDADAPMQRHLQVPLTLQRGGGLQWGIHSRGVRRREARSMASWEGPPIWTGLQLVNRWKGQGSALLAPDRPPDTPPYAPDAAVAPAQPDTKRARRTLKEACTVCRCAPGHMRQLQVTLTGDGTWRRFRLRAPQGAKRKAEVLKVATQHDERIANYTAWYLKRPEHAAGCDTCDGDSRLDGACRGCRPLLVGDQCFRRYLDKIEADRDDGLAQIKPKAQEAVAAMAAKRDARAQKVAARAAKLSEATGQRTAATRDASHEARAQKELEAVATEGTTVRHDAAAVSAFGSWVARKGDEYRHQVGVLANRLEHGLRLQELMAPDSVVADQQRASGHARVGYRYVLTAM 142AVAHPVGRGNAGSPGARGPEELPRQLVNRASNVTRPATYGCAPCRHVRLSIPKPVLTGCRACEQTTHPAPKRAVRGGADAAKYDLAAFFAGWAADLEGRNRRRQVHAPLDPQPDPNHEPAVTLQKIDLAEVSIEEFQRVLARSVKHRHDGRASREREKARAYAQVAKKRRNSHAHGARTRRAVRRQTRAVRRAHRMGANSGEILVASGAEDPVPEAIDHAAQLRRRIRACARDLEGLRHLSRRYLKTLEKPCRRPRAPDLGRARCHALVESLQAAERELEELRRCDSPDTAMRRLDAVLAAAASTDATFATGWTVVGMDLGVAPRGSAAPEVSPMEMAISVFWRKGSRRVIVSKPIAGMPIRRHELIRLEGLGTLRLDGNHYTGAGVTKGRGLSEGTEPDFREKSPSTLGFTLSDYRHESRWRPYGAKQGKTARQFFAAMSRELRALVEHQVLAPMGPPLLEAHERRFETLLKGQDNKSIHAGGGGRYVWRGPPDSKKRPAADGDWFRFGRGHADHRGWANKRHELAANYLQSAFRLWSTLAEAQEPTPYARYKYTRVTM 143WDFLTLQVYERHTSPEVCVAGNSTKCASGTRKSDHTHGVGVKLGAQEINVSANDDRDHEVGCNICVISRVSLDIKGWRYGCESCVQSTPEWRSIVRFDRNHKEAKGECLSRFEYWGAQSTARSLKRNKLMGGVNLDELAIVQNENVVKTSLKHLFDKRKDRIQANLKAVKVRMRERRKSGRQRKALRRQCRKLKRYLRSYDPSDIKEGNSCSAFTKLGLDIGISPNKPPKIEPKVEVVFSLFYQGACDKIVTVSSPESPLPRSWKIKIDGIRALYVKSTKVKFGGRTFRAGQRNNRRKVRPPNVKKGKRKGSRSQFFNKFAVGLDAVSQQLPIASVQGLWGRAETKKAQTICLK QLESNKPLKESQRCLFLADNWVVRVCGFLRALSQRQGPTPYIRYRYRCNM 144ARNVGQRNASRQSKRESAKARSRRVTGGHASVTQGVALINAAANADRDHTTGCEPCTWERVNLPLQEVIHGCDSCTKSSPFWRDIKVVNKGYREAKEEIMRIASGISADHLSRALSHNKVMGRLNLDEVCILDFRTVLDTSLKHLTDSRSNGIKEHIRAVHRKIRMRRKSGKTARALRKQYFALRRQWKAGHKPNSIREGNSLTALRAVGFDVGVSEGTEPMPAPQTEVVLSVFYKGSATRILRISSPHPIAKRSWKVKIAGIKALKLIRREHDFSFGRETYNASQRAEKRKFSPHAARKDFFNSFAVQLDRLAQQLCVSSVENLWVTEPQQKLLTLAKDTAPYGIREGARFADTRARLAWNWVFRVCGFTRALHQEQEPTPYCRFTWRSKM

In some embodiments, the Type VI CRISPR/Cas enzyme is a programmableCas13 nuclease. The general architecture of a Cas13 protein includes anN-terminal domain and two HEPN (higher eukaryotes and prokaryotesnucleotide-binding) domains separated by two helical domains (Liu etal., Cell 2017 Jan. 12; 168 (1-2):121-134.el2). The HEPN domains eachcomprise aR-X₄—H motif. Shared features across Cas13 proteins includethat upon binding of the crRNA of the guide nucleic acid to a targetnucleic acid, the protein undergoes a conformational change to bringtogether the HEPN domains and form a catalytically active RNase. (Tambeet al., Cell Rep. 2018 Jul. 24; 24(4): 1025-1036). Thus, two activatableHEPN domains are characteristic of a programmable Cas13 nuclease of thepresent disclosure. However, programmable Cas13 nucleases alsoconsistent with the present disclosure include Cas13 nucleasescomprising mutations in the HEPN domain that enhance the Cas13 proteinscleavage efficience or mutations that catalytically inactivate the HEPNdomains.

A programmable Cas13 nuclease can be a Cas13a protein (also referred toas “c2c2”), a Cas13b protein, a Cas13c protein, a Cas13d protein, or aCas13e protein. Example C2c2 proteins are set forth as SEQ ID NO: 47—SEQID NO: 52. In some cases, a subject C2c2 protein includes an amino acidsequence having 80% or more (e.g., 85% or more, 90% or more, 95% ormore, 98% or more, 99% or more, 99.5% or more, or 100%) amino acidsequence identity with the amino acid sequence set forth in any one ofSEQ ID NOs: 47—SEQ ID NO: 52. In some cases, a suitable C2c2 polypeptidecomprises an amino acid sequence having at least 80%, at least 85%, atleast 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acidsequence identity to the Listeria seeligeri C2c2 amino acid sequence setforth in SEQ ID NO: 47. In some cases, a suitable C2c2 polypeptidecomprises an amino acid sequence having at least 80%, at least 85%, atleast 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acidsequence identity to the Leptotrichia buccalis C2c2 amino acid sequenceset forth in SEQ ID NO: 48. In some cases, a suitable C2c2 polypeptidecomprises an amino acid sequence having at least 80%, at least 85%, atleast 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acidsequence identity to the Rhodobacter capsulatus C2c2 amino acid sequenceset forth in SEQ ID NO: 50. In some cases, a suitable C2c2 polypeptidecomprises an amino acid sequence having at least 80%, at least 85%, atleast 90%, at least 95%, at least 98%, at least 99%, or 10000, aminoacid sequence identity to the Carnobacterium gallinarum C2c2 amino acidsequence set forth in SEQ ID NO: 51. In some cases, a suitable C2c2polypeptide comprises an amino acid sequence having at least 80%, atleast 85%, at least 90%, at least 95%, at least 98%, at least 99%, or100%, amino acid sequence identity to the Herbinix hemicellulosilyticaC2c2 amino acid sequence set forth in SEQ ID NO: 52. In some cases, theC2c2 protein includes an amino acid sequence having 80% or more aminoacid sequence identity with the Leptotrichia buccalis (Lbu) C2c2 aminoacid sequence set forth in SEQ ID NO: 48. In some cases, the C2c2protein is a Leptotrichia buccalis (Lbu) C2c2 protein (e.g., see SEQ IDNO: 48). In some cases, the C2c2 protein includes the amino acidsequence set forth in any one of SEQ ID NOs: 47-48 and SEQ TD NOs:50-52. In some cases, a C2c2 protein used in a method of the presentdisclosure is not a Leptotrichia shahii (Lsh) C2c2 protein. In somecases, a C2c2 protein used in a method of the present disclosure is nota C2c2 polypeptide having at least 80%, at least 85%, at least 90%, atleast 95% at least 98%, at least 99% or 100%, amino acid sequenceidentity to the Lsh C2c2 polypeptide set forth in SEQ TD NO: 49. Cas13protein sequences are set forth in SEQ ID NO: 47—SEQID NO: 52 and SEQIDNO: 156—SEQID NO: 167.

TABLE 3 SEQ ID NO Description Sequence  47 Listeria seeligeriMWISIKTLIHHLGVLFFCDYMYNRREKKIIEVKTMRITKVEVDRKK C2c2 aminoVLISRDKNGGKLVYENEMQDNTEQIMHHKKSSFYKSVVNKTICRPE acid sequenceQKQMKKLVHGLLQENSQEKIKVSDVTKLNISNFLNHRFKKSLYYFPENSPDKSEEYRIEINLSQLLEDSLKKQQGTFICWESFSKDMELYINWAENYISSKTKLIKKSIRNNRIQSTESRSGQLMDRYMKDILNKNKPFDIQSVSEKYQLEKLTSALKATFKEAKKNDKEINYKLKSTLQNHERQIIEELKENSELNQFNIEIRKHLETYFPIKKTNRKVGDIRNLEIGEIQKIVNHRLKNKIVQRILQEGKLASYEIESTVNSNSLQKIKIEEAFALKFINACLFASNNLRNMVYPVCKKDILMIGEFKNSFKEIKHKKFIRQWSQFFSQEITVDDIELASWGLRGAIAPIRNEIIHLKKHSWKKFFNNPTFKVKKSKIINGKTKDVTSEFLYKETLFKDYFYSELDSVPELIINKMESSKILDYYSSDQLNQVFTIPNFELSLLTSAVPFAPSFKRVYLKGFDYQNQDEAQPDYNLKLNIYNEKAFNSEAFQAQYSLFKMVYYQVFLPQFTTNNDLFKSSVDFILTLNKERKGYAKAFQDIRKMNKDEKPSEYMSYIQSQLMLYQKKQEEKEKINHFEKFINQVFIKGFNSFIEKNRLTYICHPTKNTVPENDNIEIPFHTDMDDSNIAFWLMCKLLDAKQLSELRNEMIKFSCSLQSTEEISTFTKAREVIGLALLNGEKGCNDWKELFDDKEAWKKNMSLYVSEELLQSLPYTQEDGQTPVINRSIDLVKKYGTETILEKLFSSSDDYKVSAKDIAKLHEYDVTEKIAQQESLHKQWIEKPGLARDSAWTKKYQNVINDISNYQWAKTKVELTQVRHLHQLTIDLLSRLAGYMSIADRDFQFSSNYILERENSEYRVTSWILLSENKNKNKYNDYELYNLKNASIKVSSKNDPQLKVDLKQLRLTLEYLELFDNRLKEKRNNISHFNYLNGQLGNSILELFDDARDVLSYDRKLKNAVSKSLKEILSSHGMEVTFKPLYQTNHHLKIDKLQPKKIFIHLGEKSTVSSN QVSNEYCQLVRTLLTMK  48Leptotrichia buccalis MKVTKVGGISHKKYTSEGRLVKSESEENRTDERLSALLNMRLDMYI(Lbu) C2c2 KNPSSTETKENQKRIGKLKKFFSNKMVYLKDNTLSLKNGKKENIDR amino acidEYSETDILESDVRDKKNFAVLKKIYLNENVNSEELEVFRNDIKKKL sequenceNKINSLKYSFEKNKANYQKINENNIEKVEGKSKRNIIYDYYRESAKRDAYVSNVKEAFDKLYKEEDIAKLVLEIENLTKLEKYKIREFYHEIIGRKNDKENFAKIIYEEIQNVNNMKELIEKVPDMSELKKSQVFYKYYLDKEELNDKNIKYAFCHFVEIEMSQLLKNYVYKRLSNISNDKIKRIFEYQNLKKLIENKLLNKLDTYVRNCGKYNYYLQDGEIATSDFIARNRQNEAFLRNIIGVSSVAYFSLRNILETENENDITGRMRGKTVKNNKGEEKYVSGEVDKIYNENKKNEVKENLKMFYSYDFNMDNKNEIEDFFANIDEAISSIRHGIVHFNLELEGKDIFAFKNIAPSEISKKMFQNEINEKKLKLKIFRQLNSANVFRYLEKYKILNYLKRTRFEFVNKNIPFVPSFTKLYSRIDDLKNSLGIYWKTPKTNDDNKTKEIIDAQIYLLKNIYYGEFLNYFMSNNGNFFEISKEIIELNKNDKRNLKTGFYKLQKFEDIQEKIPKEYLANIQSLYMINAGNQDEEEKDTYIDFIQKIFLKGFMTYLANNGRLSLWIGSDEETNTSLAEKKQEFDKFLKKYEQNNNIKIPYEINEFLREIKLGNILKYTERLNMFYLILKLLNHKELTNLKGSLEKYQSANKEEAFSDQLELINLLNLDNNRVTEDFELEADEIGKFLDFNGNKVKDNKELKKFDTNKIYFDGENIIKHRAFYNIKKYGMLNLLEKIADKAGYKISIEELKKYSNKKNEIEKNHKMQENLHRKYARPRKDEKFTDEDYESYKQAIENIEEYTHLKNKVEFNELNLLQGLLLRILHRLVGYTSIWERDLRFRLKGEFPENQYIEEIFNFENKKNVKYKGGQIVEKYIKFYKELHQNDEVKINKYSSANIKVLKQEKKDLYIRNYIAHFNYIPHAEISLLEVLENLRKLLSYDRKLKNAVMKSVVDILKEYGFVATFKIGADKKIGIQTLESEKIVHLKNLKKKKLMTDRNSEELCKLVKIMFEYK MEEKKSEN  49Leptotrichia shahii MGNLFGHKRWYEVRDKKDFKIKRKVKVKRNYDGNKYILNINENNNK(Lsh) C2c3 EKIDNNKFIRKYINYKKNDNILKEFTRKFHAGNILFKLKGKEGIIR proteinIENNDDFLETEEVVLYIEAYGKSEKLKALGITKKKIIDEAIRQGITKDDKKIEIKRQENEEEIEIDIRDEYTNKTLNDCSIILRIIENDELETKKSIYEIFKNINMSLYKIIEKIIENETEKVFENRYYEEHLREKLLKDDKIDVILTNFMEIREKIKSNLEILGFVKFYLNVGGDKKKSKNKKMLVEKILNINVDLTVEDIADFVIKELEFWNITKRIEKVKKVNNEFLEKRRNRTYIKSYVLLDKHEKFKIERENKKDKIVKFFVENIKNNSIKEKIEKILAEFKIDELIKKLEKELKKGNCDTEIFGIFKKHYKVNFDSKKFSKKSDEEKELYKIIYRYLKGRIEKILVNEQKVRLKKMEKIEIEKILNESILSEKILKRVKQYTLEHIMYLGKLRHNDIDMTTVNTDDFSRLHAKEELDLELITFFASTNMELNKIFSRENINNDENIDFFGGDREKNYVLDKKILNSKIKIIRDLDFIDNKNNITNNFIRKFTKIGTNERNRILHAISKERDLQGTQDDYNKVINIIQNLKISDEEVSKALNLDVVFKDKKNIITKINDIKISEENNNDIKYLPSFSKVLPEILNLYRNNPKNEPFDTIETEKIVLNALIYVNKELYKKLILEDDLEENESKNIFLQELKKTLGNIDEIDENIIENYYKNAQISASKGNNKAIKKYQKKVIECYIGYLRKNYEELFDFSDFKMNIQEIKKQIKDINDNKTYERITVKTSDKTIVINDDFEYIISIFALLNSNAVINKIRNRFFATSVWLNTSEYQNIIDILDEIMQLNTLRNECITENWNLNLEEFIQKMKEIEKDFDDFKIQTKKEIFNNYYEDIKNNILTEFKDDINGCDVLEKKLEKIVIFDDETKFEIDKKSNILQDEQRKLSNINKKDLKKKVDQYIKDKDQEIKSKILCRIIFNSDFLKKYKKEIDNLIEDMESENENKFQEIYYPKERKNELYIYKKNLFLNIGNPNFDKIYGLISNDIKMADAKFLFNIDGKNIRKNKISEIDAILKNLNDKLNGYSKEYKEKYIKKLKENDDFFAKNIQNKNYKSFEKDYNRVSEYKKIRDLVEFNYLNKIESYLIDINWKLAIQMARFERDMHYIVNGLRELGIIKLSGYNTGISRAYPKRNGSDGFYTTTAYYKFFDEESYKKFEKICYGFGIDLSENSEINKPENESIRNYISHFYIVRNPFADYSIAEQIDRVSNLLSYSTRYNNSTYASVFEVFKKDVNLDYDELKKKFKLIGNNDILERLMKPKKVSVLELESYNSDYIKNLIIELLT KIENTNDTL  50 RhodobacterMQIGKVQGRTISEFGDPAGGLKRKISTDGKNRKELPAHLSSDPKAL capsulatusIGQWISGIDKIYRKPDSRKSDGKAIHSPTPSKMQFDARDDLGEAFW C2c2 aminoKLVSEAGLAQDSDYDQFKRRLHPYGDKFQPADSGAKLKFEADPPEP acid sequenceQAFHGRWYGAMSKRGNDAKELAAALYEHLHVDEKRIDGQPKRNPKTDKFAPGLVVARALGIESSVLPRGMARLARNWGEEEIQTYFVVDVAASVKEVAKAAVSAAQAFDPPRQVSGRSLSPKVGFALAEHLERVTGSKRCSFDPAAGPSVLALHDEVKKTYKRLCARGKNAARAFPADKTELLALMRHTHENRVRNQMVRMGRVSEYRGQQAGDLAQSHYWTSAGQTEIKESEIFVRLWVGAFALAGRSMKAWIDPMGKIVNTEKNDRDLTAAVNIRQVISNKEMVAEAMARRGIYFGETPELDRLGAEGNEGFVFALLRYLRGCRNQTFHLGARAGFLKEIRKELEKTRWGKAKEAEHVVLTDKTVAAIRAIIDNDAKALGARLLADLSGAFVAHYASKEHFSTLYSEIVKAVKDAPEVSSGLPRLKLLLKRADGVRGYVHGLRDTRKHAFATKLPPPPAPRELDDPATKARYIALLRLYDGPFRAYASGITGTALAGPAARAKEAATALAQSVNVTKAYSDVMEGRSSRLRPPNDGETLREYLSALTGETATEFRVQIGYESDSENARKQAEFIENYRRDMLAFMFEDYIRAKGFDWILKIEPGATAMTRAPVLPEPIDTRGQYEHWQAALYLVMHFVPASDVSNLLHQLRKWEALQGKYELVQDGDATDQADARREALDLVKRFRDVLVLFLKTGEARFEGRAAPFDLKPFRALFANPATFDRLFMATPTTARPAEDDPEGDGASEPELRVARTLRGLRQIARYNHMAVLSDLFAKHKVRDEEVARLAEIEDETQEKSQIVAAQELRTDLHDKVMKCHPKTISPEERQSYAAAIKTIEEHRFLVGRVYLGDHLRLHRLMMDVIGRLIDYAGAYERDTGTFLINASKQLGAGADWAVTIAGAANTDARTQTRKDLAHFNVLDRADGTPDLTALVNRAREMMAYDRKRKNAVPRSILDMLARLGLTLKWQMKDHLLQDATITQAAIKHLDKVRLTVGGPAAVTEARFSQDYLQMVAAVFNGSVQNPKPRRRDDGDAWHKPPKPATAQSQPDQKPPNKAPSAGSRLPPPQVGEVYEGVVVKVIDTGSLGFLAVEGVAGNIGLHISRLRRIREDAIIVGRRYRFRVEIYVPPKSNTSKLNAADLVRID  51 CarnobacteriumMRITKVKIKLDNKLYQVTMQKEEKYGTLKLNEESRKSTAEILRLKK gallinarumASFNKSFHSKTINSQKENKNATIKKNGDYISQIFEKLVGVDTNKNI C2c2 aminoRKPKMSLTDLKDLPKKDLALFIKRKFKNDDIVEIKNLDLISLFYNA acid sequenceLQKVPGEHFTDESWADFCQEMMPYREYKNKFIERKIILLANSIEQNKGFSINPETFSKRKRVLHQWAIEVQERGDFSILDEKLSKLAEIYNFKKMCKRVQDELNDLEKSMKKGKNPEKEKEAYKKQKNFKIKTIWKDYPYKTHIGLIEKIKENEELNQFNIEIGKYFEHYFPIKKERCTEDEPYYLNSETIATTVNYQLKNALISYLMQIGKYKQFGLENQVLDSKKLQEIGIYEGFQTKFMDACVFATSSLKNIIEPMRSGDILGKREFKEAIATSSFVNYHEIFFPYFPFELKGMKDRESELIPFGEQTEAKQMQNIWALRGSVQQIRNEIFHSFDKNQKFNLPQLDKSNFEFDASENSTGKSQSYIETDYKFLFEAEKNQLEQFFIERIKSSGALEYYPLKSLEKLFAKKEMKFSLGSQVVAFAPSYKKLVKKGHSYQTATEGTANYLGLSYYNRYELKEESFQAQYYLLKLIYQYVFLPNFSQGNSPAFRETVKAILRINKDEARKKMKKNKKFLRKYAFEQVREMEFKETPDQYMSYLQSEMREEKVRKAEKNDKGFEKNITMNFEKLLMQIFVKGFDVFLTTFAGKELLLSSEEKVIKETEISLSKKINEREKTLKASIQVEHQLVATNSAISYWLFCKLLDSRHLNELRNEMIKFKQSRIKFNHTQHAELIQNLLPIVELTILSNDYDEKNDSQNVDVSAYFEDKSLYETAPYVQTDDRTRVSFRPILKLEKYHTKSLIEALLKDNPQFRVAATDIQEWMHKREEIGELVEKRKNLHTEWAEGQQTLGAEKREEYRDYCKKIDRFNWKANKVTLTYLSQLHYLITDLLGRMVGFSALFERDLVYFSRSFSELGGETYHISDYKNLSGVLRLNAEVKPIKIKNIKVIDNEENPYKGNEPEVKPFLDRLHAYLENVIGIKAVHGKIRNQTAHLSVLQLELSMIESMNNLRDLMAYDRKLKNAVTKSMIKILDKHGMILKLKIDENHKNFEIESLIPKEIIHLKDKAIKTNQVSEEYCQLVLALLTTNPGNQLN  52 HerbinixMKLTRRRISGNSVDQKITAAFYRDMSQGLLYYDSEDNDCTDKVIES hemicellulosilyticaMDFERSWRGRILKNGEDDKNPFYMFVKGLVGSNDKIVCEPIDVDSD C2c2 aminoPDNLDILINKNLTGFGRNLKAPDSNDTLENLIRKIQAGIPEEEVLP acid sequenceELKKIKEMIQKDIVNRKEQLLKSIKNNRIPFSLEGSKLVPSTKKMKWLFKLIDVPNKTFNEKMLEKYWEIYDYDKLKANITNRLDKTDKKARSISRAVSEELREYHKNLRTNYNRFVSGDRPAAGLDNGGSAKYNPDKEEFLLFLKEVEQYFKKYFPVKSKHSNKSKDKSLVDKYKNYCSYKVVKKEVNRSIINQLVAGLIQQGKLLYYFYYNDTWQEDFLNSYGLSYIQVEEAFKKSVMTSLSWGINRLTSFFIDDSNTVKFDDITTKKAKEAIESNYFNKLRTCSRMQDHFKEKLAFFYPVYVKDKKDRPDDDIENLIVLVKNAIESVSYLRNRTFHFKESSLLELLKELDDKNSGQNKIDYSVAAEFIKRDIENLYDVFREQIRSLGIAEYYKADMISDCFKTCGLEFALYSPKNSLMPAFKNVYKRGANLNKAYIRDKGPKETGDQGQNSYKALEEYRELTWYIEVKNNDQSYNAYKNLLQLIYYHAFLPEVRENEALITDFINRTKEWNRKETEERLNTKNNKKHKNFDENDDITVNTYRYESIPDYQGESLDDYLKVLQRKQMARAKEVNEKEEGNNNYIQFIRDVVVWAFGAYLENKLKNYKNELQPPLSKENIGLNDTLKELFPEEKVKSPFNIKCRFSISTFIDNKGKSTDNTSAEAVKTDGKEDEKDKKNIKRKDLLCFYLFLRLLDENEICKLQHQFIKYRCSLKERRFPGNRTKLEKETELLAELEELMELVRFTMPSIPEISAKAESGYDTMIKKYFKDFIEKKVFKNPKTSNLYYHSDSKTPVTRKYMALLMRSAPLHLYKDIFKGYYLITKKECLEYIKLSNIIKDYQNSLNELHEQLERIKLKSEKQNGKDSLYLDKKDFYKVKEYVENLEQVARYKHLQHKINFESLYRIFRIHVDIAARMVGYTQDWERDMHFLFKALVYNGVLEERRFEAIFNNNDDNNDGRIVKKIQNNLNNKNRELVSMLCWNKKLNKNEFGAIIWKRNPIAHLNHFTQTEQNSKSSLESLINSLRILLAYDRKRQNAVTKTINDLLLNDYHIRIKWEGRVDEGQIYFNIKEKEDIENEPIIHLKHLHKKDCYIYKNSYMFDKQKEWICNGIKEEVYDKSILKCIGNLFKFDYEDKNKSSANPKHT 156 PaludibacterMRVSKVKVKDGGKDKMVLVHRKTTGAQLVYSGQPVSNETSNILPEK propionicigenesKRQSFDLSTLNKTIIKFDTAKKQKLNVDQYKIVEKIFKYPKQELPK C2c2 aminoQIKAEEILPFLNHKFQEPVKYWKNGKEESFNLTLLIVEAVQAQDKR acid sequenceKLQPYYDWKTWYIQTKSDLLKKSIENNRIDLTENLSKRKKALLAWETEFTASGSIDLTHYHKVYMTDVLCKMLQDVKPLTDDKGKINTNAYHRGLKKALQNHQPAIFGTREVPNEANRADNQLSIYHLEVVKYLEHYFPIKTSKRRNTADDIAHYLKAQTLKTTIEKQLVNAIRANIIQQGKTNHHELKADTTSNDLIRIKTNEAFVLNLTGTCAFAANNIRNMVDNEQTNDILGKGDFIKSLLKDNTNSQLYSFFFGEGLSTNKAEKETQLWGIRGAVQQIRNNVNHYKKDALKTVFNISNFENPTITDPKQQTNYADTIYKARFINELEKIPEAFAQQLKTGGAVSYYTIENLKSLLTTFQFSLCRSTIPFAPGFKKVFNGGINYQNAKQDESFYELMLEQYLRKENFAEESYNARYFMLKLIYNNLFLPGFTTDRKAFADSVGFVQMQNKKQAEKVNPRKKEAYAFEAVRPMTAADSIADYMAYVQSELMQEQNKKEEKVAEETRINFEKFVLQVFIKGFDSFLRAKEFDFVQMPQPQLTATASNQQKADKLNQLEASITADCKLTPQYAKADDATHIAFYVFCKLLDAAHLSNLRNELIKFRESVNEFKFFIHLLEIIEICLLSADVVPTDYRDLYSSEADCLARLRPFIEQGADITNWSDLFVQSDKHSPVIHANIELSVKYGTTKLLEQIINKDTQFKTTEANFTAWNTAQKSIEQLIKQREDHHEQWVKAKNADDKEKQERKREKSNFAQKFIEKHGDDYLDICDYINTYNWLDNKMHFVIALNRLHGLTIELLGRMAGFVALFDRDFQFFDEQQIADEFKLHGFVNLHSIDKKLNEVPTKKIKEIYDIRNKIIQINGNKINESVRANLIQFISSKRNYYNNAFLHVSNDEIKEKQMYDIRNHIAHFNYLTKDAADFSLIDLINELRELLHYDRKLKNAVSKAFIDLFDKHGMILKLKLNADHKLKVESLEPKKIYHLGSSAKDKPEYQYCTNQVMMAYCNMCRS LLEMKK 157Leptotrichia wadei MYMKITKIDGVSHYKKQDKGILKKKWKDLDERKQREKIEARYNKQI(Lwa) C2c2 ESKIYKEFFRLKNKKRIEKEEDQNIKSLYFFIKELYLNEKNEEWEL amino acidKNINLEILDDKERVIKGYKFKEDVYFFKEGYKEYYLRILFNNLIEK sequenceVQNENREKVRKNKEFLDLKEIFKKYKNRKIDLLLKSINNNKINLEYKKENVNEEIYGINPTNDREMTFYELLKEIIEKKDEQKSILEEKLDNFDITNFLENIEKIFNEETEINIIKGKVLNELREYIKEKEENNSDNKLKQIYNLELKKYIENNFSYKKQKSKSKNGKNDYLYLNFLKKIMFIEEVDEKKEINKEKFKNKINSNFKNLFVQHILDYGKLLYYKENDEYIKNTGQLETKDLEYIKTKETLIRKMAVLVSFAANSYYNLFGRVSGDILGTEVVKSSKTNVIKVGSHIFKEKMLNYFFDFEIFDANKIVEILESISYSIYNVRNGVGHFNKLILGKYKKKDINTNKRIEEDLNNNEEIKGYFIKKRGEIERKVKEKFLSNNLQYYYSKEKIENYFEVYEFEILKRKIPFAPNFKR11KKGEDLFNNKNNKKYEYFKNFDKNSAEEKKEFLKTRNFLLKELYYNNFYKEFLSKKEEFEKIVLEVKEEKKSRGNINNKKSGVSFQSIDDYDTKINISDYIASIHKKEMERVEKYNEEKQKDTAKYIRDFVEEIFLTGFINYLEKDKRLHFLKEEFSILCNNNNNVVDFNININEEKIKEFLKENDSKTLNLYLFFNMIDSKRISEFRNELVKYKQFTKKRLDEEKEFLGIKIELYETLIEFVILTREKLDTKKSEEIDAWLVDKLYVKDSNEYKEYEEILKLFVDEKILSSKEAPYYATDNKTPILLSNFEKTRKYGTQSFLSEIQSNYKYSKVEKENIEDYNKKEEIEQKKKSNIEKLQDLKVELHKKWEQNKITEKEIEKYNNTTRKINEYNYLKNKEELQNVYLLHEMLSDLLARNVAFFNKWERDFKFIVIAIKQFLRENDKEKVNEFLNPPDNSKGKKVYFSVSKYKNTVENIDGIHKNFMNLIFLNNKFMNRKIDKMNCAIWVYFRNYIAHFLHLHTKNEKISLISQMNLLIKLFSYDKKVQNHILKSTKTLLEKYNIQINFEISNDKNEVFKYKIKNRLYSKKGKMLGKNNKFEILENEFLENVKAMLEYSE 158 BergeyellaMENKTSLGNNIYYNPFKPQDKSYFAGYFNAAMENTDSVFRELGKRL zoohelcumKGKEYTSENFFDAIFKENISLVEYERYVKLLSDYFPMARLLDKKEV Cas13bPIKERKENFKKNFKGIIKAVRDLRNFYTHKEHGEVEITDEIFGVLDEMLKSTVLTVKKKKVKTDKTKEILKKSIEKQLDILCQKKLEYLRDTARKIEEKRRNQRERGEKELVAPFKYSDKRDDLIAAIYNDAFDVYIDKKKDSLKESSKAKYNTKSDPQQEEGDLKIPISKNGVVFLLSLFLTKQEIHAFKSKIAGFKATVIDEATVSEATVSHGKNSICFMATHEIFSHLAYKKLKRKVRTAEINYGEAENAEQLSVYAKETLMMQMLDELSKVPDVVYQNLSEDVQKTFIEDWNEYLKENNGDVGTMEEEQVIHPVIRKRYEDKFNYFAIRFLDEFAQFPTLRFQVHLGNYLHDSRPKENLISDRRIKEKITVFGRLSELEHKKALFIKNTETNEDREHYWEIFPNPNYDFPKENISVNDKDFPIAGSILDREKQPVAGKIGIKVKLLNQQYVSEVDKAVKAHQLKQRKASKPSIQNIIEEIVPINESNPKEAIVFGGQPTAYLSMNDIHSILYEFFDKWEKKKEKLEKKGEKELRKEIGKELEKKIVGKIQAQIQQIIDKDTNAKILKPYQDGNSTAIDKEKLIKDLKQEQNILQKLKDEQTVREKEYNDFIAYQDKNREINKVRDRNHKQYLKDNLKRKYPEAPARKEVLYYREKGKVAVWLANDIKRFMPTDFKNEWKGEQHSLLQKSLAYYEQCKEELKNLLPEKVFQHLPFKLGGYFQQKYLYQFYTCYLDKRLEYISGLVQQAENFKSENKVFKKVENECFKFLKKQNYTHKELDARVQSILGYPIFLERGFMDEKPTIIKGKTFKGNEALFADWFRYYKEYQNFQTFYDTENYPLVELEKKQADRKRKTKIYQQKKNDVFTLLMAKHIFKSVFKQDSIDQFSLEDLYQSREERLGNQERARQTGERNTNYIWNKTVDLKLCDGKITVENVKLKNVGDFIKYEYDQRVQAFLKYEENIEWQAFLIKESKEEENYPYVVEREIEQYEKVRREELLKEVHLIEEYILEKVKDKEILKKGDNQNFKYYILNGLLKQLKNEDVESYKVFNLNTEPEDVNINQLKQEATDLEQKAFVLTYIRNKFAHNQLPKKEFWDYCQEKYGKIEKEKTYAEYFAEVFKKEKEALIK 159 PrevotellaMEDDKKTTDSIRYELKDKHFWAAFLNLARHNVYITVNHINKILEEG intermediaEINRDGYETTLKNTWNEIKDINKKDRLSKLIIKHFPFLEAATYRLN Cas13bPTDTTKQKEEKQAEAQSLESLRKSFFVFIYKLRDLRNHYSHYKHSKSLERPKFEEGLLEKMYNIFNASIRLVKEDYQYNKDINPDEDFKHLDRTEEEFNYYFTKDNEGNITESGLLFFVSLFLEKKDAIWMQQKLRGFKDNRENKKKMTNEVFCRSRMLLPKLRLQSTQTQDWILLDMLNELIRCPKSLYERLREEDREKFRVPIEIADEDYDAEQEPFKNTLVRHQDRFPYFALRYFDYNEIFTNLRFQIDLGTYHFSIYKKQIGDYKESHEILTHKLYGFERIQEFTKQNRPDEWRKFVKTFNSFETSKEPYIPETTPHYHLENQKIGIRFRNDNDKIWPSLKTNSEKNEKSKYKLDKSFQAEAFLSVHELLPMMFYYLLLKTENTDNDNEIETKKKENKNDKQEKHKIEEIIENKITEIYALYDTFANGEIKSIDELEEYCKGKDIEIGHLPKQMIAILKDEHKVMATEAERKQEEMLVDVQKSLESLDNQINEEIENVERKNSSLKSGKIASWLVNDMMRFQPVQKDNEGKPLNNSKANSTEYQLLQRTLAFFGSEHERLAPYFKQTKLIESSNPHPFLKDTEWEKCNNILSFYRSYLEAKKNFLESLKPEDWEKNQYFLKLKEPKTKPKTLVQGWKNGFNLPRGIFTEPIRKWFMKHRENITVAELKRVGLVAKVIPLFFSEEYKDSVQPFYNYHFNVGNINKPDEKNFLNCEERRELLRKKKDEFKKMTDKEKEENPSYLEFKSWNKFERELRLVRNQDIVTWLLCMELFNKKKIKELNVEKIYLKNINTNTTKKEKNTEEKNGEEKNIKEKNNILNRIMPMRLPIKVYGRENFSKNKKKKIRRNTFFTVYIEEKGTKLLKQGNFKALERDRRLGGLFSFVKTPSKAESKSNTISKLRVEYELGEYQKARIEIIKDMLALEKTLIDKYNSLDTDNFNKMLTDWLELKGEPDKASFQNDVDLLIAVRNAFSHNQYPMRNRIAFANINPFSLSSANTSEEKGLGIANQ LKDKTHKTIEKIIEIEKPIETKE160 Prevotella buccae MQKQDKLFVDRKKNAIFAFPKYITIMENKEKPEPIYYELTDKHFWACas13b AFLNLARHNVYTTINHINRRLEIAELKDDGYMMGIKGSWNEQAKKLDKKVRLRDLIMKHFPFLEAAAYEMTNSKSPNNKEQREKEQSEALSLNNLKNVLFIFLEKLQVLRNYYSHYKYSEESPKPIFETSLLKNMYKVFDANVRLVKRDYMHHENIDMQRDFTHLNRKKQVGRTKNIIDSPNFHYHFADKEGNMTIAGLLFFVSLFLDKKDAIWMQKKLKGFKDGRNLREQMTNEVFCRSRISLPKLKLENVQTKDWMQLDMLNELVRCPKSLYERLREKDRESFKVPFDIFSDDYNAEEEPFKNTLVRHQDRFPYFVLRYFDLNEIFEQLRFQIDLGTYHFSIYNKRIGDEDEVRHLTHHLYGFARIQDFAPQNQPEEWRKLVKDLDHFETSQEPYISKTAPHYHLENEKIGIKFCSAHNNLFPSLQTDKTCNGRSKFNLGTQFTAEAFLSVHELLPMMFYYLLLTKDYSRKESADKVEGIIRKEISNIYAIYDAFANNEINSIADLTRRLQNTNILQGHLPKQMISILKGRQKDMGKEAERKIGEMIDDTQRRLDLLCKQTNQKIRIGKRNAGLLKSGKIADWLVNDMMRFQPVQKDQNNIPINNSKANSTEYRMLQRALALFGSENFRLKAYFNQMNLVGNDNPHPFLAETQWEHQTNILSFYRNYLEARKKYLKGLKPQNWKQYQHFLILKVQKTNRNTLVTGWKNSFNLPRGIFTQPIREWFEKHNNSKRIYDQILSFDRVGFVAKAIPLYFAEEYKDNVQPFYDYPFNIGNRLKPKKRQFLDKKERVELWQKNKELFKNYPSEKKKTDLAYLDFLSWKKFERELRLIKNQDIVTWLMFKELFNMATVEGLKIGEIHLRDIDTNTANEESNNILNRIMPMKLPVKTYETDNKGNILKERPLATFYIEETETKVLKQGNFKALVKDRRLNGLFSFAETTDLNLEEHPISKLSVDLELIKYQTTRISIFEMTLGLEKKLIDKYSTLPTDSFRNMLERWLQCKANRPELKNYVNSLIAVRNAFSHNQYPMYDATLFAEVKKFTLFPSVDTKKIELN IAPQLLEIVGKAIKEIEKSENKN161 Porphyromonas MNTVPASENKGQSRTVEDDPQYFGLYLNLARENLIEVESHVRIKFGgingivalix KKKLNEESLKQSLLCDHLLSVDRWTKVYGHSRRYLPFLHYFDPDSQ Cas13bEKDHDSKTGVDPDSAQRLIRELYSLLDFLRNDFSHNRLDGTTFEHLEVSPDISSFITGTYSLACGRAQSRFAVFFKPDDFVLAKNRKEQLISVADGKECLTVSGFAFFICLFLDREQASGMLSRIRGFKRTDENWARAVHETFCDLCIRHPHDRLESSNTKEALLLDMLNELNRCPRILYDMLPEEERAQFLPALDENSMNNLSENSLDEESRLLWDGSSDWAEALTKRIRHQDRFPYLMLRFIEEMDLLKGIRFRVDLGEIELDSYSKKVGRNGEYDRTITDHALAFGKLSDFQNEEEVSRMISGEASYPVRFSLFAPRYAIYDNKIGYCHTSDPVYPKSKTGEKRALSNPQSMGFISVHDLRKLLLMELLCEGSFSRMQSDFLRKANRILDETAEGKLQFSALFPEMRHRFIPPQNPKSKDRREKAETTLEKYKQEIKGRKDKLNSQLLSAFDMDQRQLPSRLLDEWMNIRPASHSVKLRTYVKQLNEDCRLRLRKFRKDGDGKARAIPLVGEMATFLSQDIVRMIISEETKKLITSAYYNEMQRSLAQYAGEENRRQFRAIVAELRLLDPSSGHPFLSATMETAHRYTEGFYKCYLEKKREWLAKIFYRPEQDENTKRRISVFFVPDGEARKLLPLLIRRRMKEQNDLQDWIRNKQAHPIDLPSHLFDSKVMELLKVKDGKKKWNEAFKDWWSTKYPDGMQPFYGLRRELNIHGKSVSYIPSDGKKFADCYTHLMEKTVRDKKRELRTAGKPVPPDLAADIKRSFHRAVNEREFMLRLVQEDDRLMLMAINKMMTDREEDILPGLKNIDSILDEENQFSLAVHAKVLEKEGEGGDNSLSLVPATIEIKSKRKDWSKYIRYRYDRRVPGLMSHFPEHKATLDEVKTLLGEYDRCRIKIFDWAFALEGAIMSDRDLKPYLHESSSREGKSGEHSTLVKMLVEKKGCLTPDESQYLILIRNKAAHNQFPCAAEMPLIYRDVSAKVGSIEGSSAKDLPEGSSLVDSLWKKYEMIIRKILPILDPENRFFGKLLNNMSQPINDL 162 BacteroidesMESIKNSQKSTGKTLQKDPPYFGLYLNMALLNVRKVENHIRKWLGD pyogenesVALLPEKSGFHSLLTTDNLSSAKWTRFYYKSRKFLPFLEMFDSDKK Cas13bSYENRRETAECLDTIDRQKISSLLKEVYGKLQDIRNAFSHYHIDDQSVKHTALIISSEMHRFIENAYSFALQKTRARFTGVFVETDFLQAEEKGDNKKFFAIGGNEGIKLKDNALIFLICLFLDREEAFKFLSRATGFKSTKEKGFLAVRETFCALCCRQPHERLLSVNPREALLMDMLNELNRPDILFEMLDEKDQKSFLPLLGEEEQAHILENSLNDELCEAIDDPFEMIASLSKRVRYKNRFPYLMLRYIEEKNLLPFIRFRIDLGCLELASYPKKMGEENNYERSVTDHAMAFGRLTDFHNEDAVLQQITKGITDEVRFSLYAPRYAIYNNKIGFVRTSGSDKISFPTLKKKGGEGHCVAYTLQNTKSFGFISIYDLRKILLLSFLDKDKAKNIVSGLLEQCEKHWKDLSENLFDAIRTELQKEFPVPLIRYTLPRSKGGKLVSSKLADKQEKYESEFERRKEKLTEILSEKDFDLSQIPRRMIDEWLNVLPTSREKKLKGYVETLKLDCRERLRVFEKREKGEHPLPPRIGEMATDLAKDIIRMVIDQGVKQRITSAYYSEIQRCLAQYAGDDNRRHLDSIIRELRLKDTKNGHPFLGKVLRPGLGHTEKLYQRYFEEKKEWLEATFYPAASPKRVPRFVNPPTGKQKELPLIIRNLMKERPEWRDWKQRKNSHPIDLPSQLFENEICRLLKDKIGKEPSGKLKWNEMFKLYWDKEFPNGMQRFYRCKRRVEVFDKVVEYEYSEEGGNYKKYYEALIDEVVRQKISSSKEKSKLQVEDLTLSVRRVFKRAINEKEYQLRLLCEDDRLLFMAVRDLYDWKEAQLDLDKIDNMLGEPVSVSQVIQLEGGQPDAVIKAECKLKDVSKLMRYCYDGRVKGLMPYFANHEATQEQVEMELRHYEDHRRRVFNWVFALEKSVLKNEKLRRFYEESQGGCEHRRCIDALRKASLVSEEEYEFLVHIRNKSAHNQFPDLEIGKLPPNVTSGFCECIWSKYKAIICRIIPFIDPER RFFGKLLEQK 163 Cas13cMTEKKSIIFKNKSSVEIVKKDIFSQTPDNMIRNYKITLKISEKNPRVVEAEIEDLMNSTILKDGRRSARREKSMTERKLIEEKVAENYSLLANCPMEEVDSIKIYKIKRFLTYRSNMLLYFASINSFLCEGIKGKDNETEEIWHLKDNDVRKEKVKENFKNKLIQSTENYNSSLKNQIEEKEKLLRKESKKGAFYRTIIKKLQQERIKELSEKSLTEDCEKIIKLYSELRHPLMHYDYQYFENLFENKENSELTKNLNLDIFKSLPLVRKMKLNNKVNYLEDNDTLFVLQKTKKAKTLYQIYDALCEQKNGFNKFINDFFVSDGEENTVFKQIINEKFQSEMEFLEKRISESEKKNEKLKKKFDSMKAHFHNINSEDTKEAYFWDIHSSSNYKTKYNERKNLVNEYTELLGSSKEKKLLREEITQINRKLLKLKQEMEEITKKNSLFRLEYKMKIAFGFLFCEFDGNISKFKDEFDASNQEKIIQYHKNGEKYLTYFLKEEEKEKFNLEKMQKIIQKTEEEDWLLPETKNNLFKFYLLTYLLLPYELKGDFLGFVKKHYYDIKNVDFMDENQNNIQVSQTVEKQEDYFYHKIRLFEKNTKKYEIVKYSIVPNEKLKQYFEDLGIDIKYLTGSVESGEKWLGENL GIDIKYLTVEQKSEVSEEKIKKFL164 Cas13c MEKDKKGEKIDISQEMIEEDLRKILILFSRLRHSMVHYDYEFYQALYSGKDFVISDKNNLENRMISQLLDLNIFKELSKVKLIKDKAISNYLDKNTTIHVLGQDIKAIRLLDIYRDICGSKNGFNKFINTMITISGEEDREYKEKVIEHFNKKMENLSTYLEKLEKQDNAKRNNKRVYNLLKQKLIEQQKLKEWFGGPYVYDIHSSKRYKELYIERKKLVDRHSKLFEEGLDEKNKKELTKINDELSKLNSEMKEMTKLNSKYRLQYKLQLAFGFILEEFDLNIDTFINNFDKDKDLIISNFMKKRDIYLNRVLDRGDNRLKNIIKEYKFRDTEDIFCNDRDNNLVKLYILMYILLPVEIRGDFLGFVKKNYYDMKHVDFIDKKDKEDKDTFFHDLRLFEKNIRKLEITDYSLSSGFLSKEHKVDIEKKINDFINRNGAMKLPEDITIEEFNKSLILPIMKNYQINFKLLNDIEISALFKIAKDRSITFKQAIDEIKNEDIKKNSKKNDKNNHKDKNINFTQLMKRALHEKIPYKAGMYQIRNNISHIDMEQLYIDPLNSYMNSNKNNITISEQIEKIIDVCVTGGVTGKELNNNIINDYYMKKEKLVFNLKLRKQNDIVSIESQEKNKREEFVFKKYGLDYKDGEINIIEVIQKVNSLQEELRNIKETSKEKLKNKETLFRDISLINGTIRKNINFKIKEMVLDIVRMDEIRHINIHIYYKGENYTRSNIIKFKYAIDGENKKYYLKQHEINDINLELKDKFVTLICNMDKHPNKNKQTIN LESNYIQNVKFIIP 165 Cas13cMENKGNNKKIDFDENYNILVAQIKEYFTKEIENYNNRIDNIIDKKELLKYSEKKEESEKNKKLEELNKLKSQKLKILTDEEIKADVIKIIKIFSDLRHSLMHYEYKYFENLFENKKNEELAELLNLNLFKNLTLLRQMKIENKTNYLEGREEFNIIGKNIKAKEVLGHYNLLAEQKNGFNNFINSFFVQDGTENLEFKKLIDEHFVNAKKRLERNIKKSKKLEKELEKMEQHYQRLNCAYVWDIHTSTTYKKLYNKRKSLIEEYNKQINEIKDKEVITAINVELLRIKKEMEEITKSNSLFRLKYKMQIAYAFLEIEFGGNIAKFKDEFDCSKMEEVQKYLKKGVKYLKYYKDKEAQKNYEFPFEEIFENKDTHNEEWLENTSENNLFKFYILTYLLLPMEFKGDFLGVVKKHYYDIKNVDFTDESEKELSQVQLDKMIGDSFFHKIRLFEKNTKRYEIIKYSILTSDEIKRYFRLLELDVPYFEYEKGTDEIGIFNKNIILTIFKYYQIIFRLYNDLEIHGLFNISSDLDKILRDLKSYGNKNINFREFLYVIKQNNNSSTEEEYRKIWENLEAKYLRLHLLTPEKEEIKTKTKEELEKLNEISNLRNGICHLNYKEIIEEILKTEISEKNKEATLNEKIRKVINFIKENELDKVELGFNFINDFFMKKEQFMFGQIKQVKEGNSDSITTERERKEKNNKKLKETYELNCDNLSEFYETSNNLRERANSSSLLEDSAFLKKIGLYKVKNNKVNSKVKDEEKRIENIKRKLLKDSSDIMGMYKAEVVKKLKEKLILIFKHDEEKRIYVTVYDTSKAVPENISKEILVKRNNSKEEYFFEDNNKKYVTEYYTLEITETNELKVIPAKKLEGKEFK TEKNKENKLMLNNHYCFNVKIIY166 Cas13c MEEIKHKKNKSSIIRVIVSNYDMTGIKEIKVLYQKQGGVDTFNLKTIINLESGNLEIISCKPKEREKYRYEFNCKTEINTISITKKDKVLKKEIRKYSLELYFKNEKKDTVVAKVTDLLKAPDKIEGERNHLRKLSSSTERKLLSKTLCKNYSEISKTPIEEIDSIKIYKIKRFLNYRSNFLIYFALINDFLCAGVKEDDINEVWLIQDKEHTAFLENRIEKITDYIFDKLSKDIENKKNQFEKRIKKYKTSLEELKTETLEKNKTFYIDSIKTKITNLENKITELSLYNSKESLKEDLIKIISIFTNLRHSLMHYDYKSFENLFENIENEELKNLLDLNLFKSIRMSDEFKTKNRTNYLDGTESFTIVKKHQNLKKLYTYYNNLCDKKNGFNTFINSFFVTDGIENTDFKNLIILHFEKEMEEYKKSIEYYKIKISNEKNKSKKEKLKEKIDLLQSELINMREHKNLLKQIYFFDIHNSIKYKELYSERKNLIEQYNLQINGVKDVTAINHINTKLLSLKNKMDKITKQNSLYRLKYKLKIAYSFLMIEFDGDVSKFKNNFDPTNLEKRVEYLDKKEEYLNYTAPKNKFNFAKLEEELQKIQSTSEMGADYLNVSPENNLFKFYILTYIMLPVEFKGDFLGFVKNHYYNIKNVDFMDESLLDENEVDSNKLNEKIENLKDSSFFNKIRLFEKNIKKYEIVKYSVSTQENMKEYFKQLNLDIPYLDYKSTDEIGIFNKNMILPIFKYYQNVFKLCNDIEIHALLALANKKQQNLEYAIYCCSKKNSLNYNELLKTFNRKTYQNLSFIRNKIAHLNYKELFSDLFNNELDLNTKVRCLIEFSQNNKFDQIDLGMNFINDYYMKKTRFIFNQRRLRDLNVPSKEKIIDGKRKQQNDSNNELLKKYGLSRTNIKDIFNKAWY 167 Cas13cMKVRYRKQAQLDTFIIKTEIVNNDIFIKSIIEKAREKYRYSFLFDGEEKYHFKNKSSVEIVKNDIFSQTPDNMIRNYKITLKISEKNPRVVEAEIEDLMNSTILKDGRRSARREKSMTERKLIEEKVAENYSLLANCPIEEVDSIKIYKIKRFLTYRSNMLLYFASINSFLCEGIKGKDNETEEIWHLKDNDVRKEKVKENFKNKLIQSTENYNSSLKNQIEEKEKLSSKEFKKGAFYRTIIKKLQQERIKELSEKSLTEDCEKIIKLYSELRHPLMHYDYQYFENLFENKENSELTKNLNLDIFKSLPLVRKMKLNNKVNYLEDNDTLFVLQKTKKAKTLYQIYDALCEQKNGFNKFINDFFVSDGEENTVFKQTINEKFQSEMEFLEKRISESEKKNEKLKKKLDSMKAHFRNINSEDTKEAYFWDIHSSRNYKTKYNERKNLVNEYTKLLGSSKEKKLLREEITKINRQLLKLKQEMEEITKKNSLFRLEYKMKIAFGFLFCEFDGNISKFKDEFDASNQEKIIQYHKNGEKYLTSFLKEEEKEKFNLEKMQKIIQKTEEEDWLLPETKNNLFKFYLLTYLLLPYELKGDFLGFVKKHYYDIKNVDFMDENQNNIQVSQTVEKQEDYFYHKIRLFEKNTKKYEIVKYSIVPNEKLKQYFEDLGIDIKYLTGSVESGEKWLGENLGIDIKYLTVEQKSEVSEEKNKKVSLKNNGMFNKTILLFVFKYYQIAFKLFNDIELYSLFFLREKSEKPFEVFLEELKDKMIGKQLNFGQLLYVVYEVLVKNKDLDKILSKKIDYRKDKSFSPEIAYLRNFLSHLNYSKFLDNFMKINTNKSDENKEVLIPSIKIQKMIQFIEKCNLQNQIDFDFNFVNDFYMRKEKMFFIQLKQIFPDINSTEKQKKSEKEEILRKRYHLINKKNEQIKDEHEAQSQLYEKILSLQKIFSCDKNNFYRRLKEEKLLFLEKQGKKKISMKEIKDKIASDISDLLGILKKEITRDIKDKLTEKFRYCEEKLLNISFYNHQDKKKEEGIRVFLIRDKNSDNFKFESILDDGSNKIFISKNGKEITIQCCDKVLETLMIEKNTLKISSNGKIISLIPHYSY SIDVKY

The programmable nuclease can be Cas13. Sometimes the Cas13 can beCas13a, Cas13b, Cas13c, Cas13d, or Cas13e. In some cases, theprogrammable nuclease can be Mad7 or Mad2. In some cases, theprogrammable nuclease can be Cas12. Sometimes the Cas12 can be Cas12a,Cas12b, Cas12c, Cas12d, or Cas12e. In some cases, the Cas12 can beCas12M08, which is a specific protein variant within the Cas12 proteinfamily/classification) In some cases, the programmable nuclease can beCsm1, Cas9, C2c4, C2c8, C2c5, C2c10, C2c9, or CasZ. Sometimes, the Csm1can also be also called smCms1, miCms1, obCms1, or suCms1. SometimesCas13a can also be also called C2c2. Sometimes CasZ can also be calledCas14a, Cas14b, Cas14c, Cas14d, Cas14e, Cas14f, Cas14g, or Cas14h.Sometimes, the programmable nuclease can be a type V CRISPR-Cas system.In some cases, the programmable nuclease can be a type VI CRISPR-Cassystem. Sometimes the programmable nuclease can be a type III CRISPR-Cassystem. In some cases, the programmable nuclease can be from at leastone of Leptotrichia shahii (Lsh), Listeria seeligeri (Lse), Leptotrichiabuccalis (Lbu), Leptotrichia wadeu (Lwa), Rhodobacter capsulatus (Rca),Herbinix hemicellulosilytica (Hhe), Paludibacter propionicigenes (Ppr),Lachnospiraceae bacterium (Lba), [Eubacterium] rectale (Ere), Listerianewyorkensis (Lny), Clostridium aminophilum (Cam), Prevotella sp. (Psm),Capnocytophaga canimorsus (Cca, Lachnospiraceae bacterium (Lba),Bergeyella zoohelcum (Bzo), Prevotella intermedia (Pin), Prevotellabuccae (Pbu), Alistipes sp. (Asp), Riemerella anatipestifer (Ran),Prevotella aurantiaca (Pau), Prevotella saccharolytica (Psa), Prevotellaintermedia (Pin2), Capnocytophaga canimorsus (Cca), Porphyromonas gulae(Pgu), Prevotella sp. (Psp), Porphyromonas gingivalis (Pig), Prevotellaintermedia (Pin3), Enterococcus italicus (Ei), Lactobacillus salivarius(Ls), or Thermus thermophilus (Tt). Sometimes the Cas13 is at least oneof LbuCas13a, LwaCas13a, LbaCas13a, HheCas13a, PprCas13a, EreCas13a,CamCas13a, or LshCas13a. The trans cleavage activity of the CRISPRenzyme can be activated when the crRNA is complexed with the targetnucleic acid. The trans cleavage activity of the CRISPR enzyme can beactivated when the guide nucleic acid comprising a tracrRNA and crRNAare complexed with the target nucleic acid. The target nucleic acid canbe RNA or DNA.

In some embodiments, a programmable nuclease as disclosed herein is anRNA-activated programmable RNA nuclease. In some embodiments, aprogrammable nuclease as disclosed herein is a DNA-activatedprogrammable RNA nuclease. In some embodiments, a programmable nucleaseis capable of being activated by a target RNA to initiate trans cleavageof an RNA reporter and is capable of being activated by a target DNA toinitiate trans cleavage of an RNA reporter, such as a Type VI CRISPR/Casenzyme (e.g., a Cas13 nuclease). For example, Cas13a of the presentdisclosure can be activated by a target RNA to initiate trans cleavageactivity of the Cas13a for the cleavage of an RNA reporter and can beactivated by a target DNA to initiate trans cleavage activity of theCas13a for trans cleavage of an RNA reporter. An RNA reporter can be anRNA-based reporter molecule. In some embodiments, the Cas13a recognizesand detects ssDNA to initiatetranscleavage of RNA reporters. MultipleCas13a isolates can recognize, be activated by, and detect target DNA,including ssDNA, upon hybridization of a guide nucleic acid with thetarget DNA. For example, Lbu-Cas13a and Lwa-Cas13a can both be activatedto transcollaterally cleave RNA reporters by target DNA. Thus, Type VICRISPR/Cas enzyme (e.g., a Cas13 nuclease, such as Cas13a) can beDNA-activated programmable RNA nucleases, and therefore, can be used todetect a target DNA using the methods as described herein. DNA-activatedprogrammable RNA nuclease detection of ssDNA can be robust at multiplepH values. For example, target ssDNA detection by Cas13 can exhibitconsistent cleavage across a wide range of pH conditions, such as from apH of 6.8 to a pH of 8.2. In contrast, target RNA detection by Cas13 mayexhibit high cleavage activity of pH values from 7.9 to 8.2. In someembodiments, a DNA-activated programmable RNA nuclease that also iscapable of being an RNA-activated programmable RNA nuclease, can haveDNA targeting preferences that are distinct from its RNA targetingpreferences. For example, the optimal ssDNA targets for Cas13a havedifferent properties than optimal RNA targets for Cas13a. As oneexample, gRNA performance on ssDNA may not necessarily correlate withthe performance of the same gRNAs on RNA. As another example, gRNAs canperform at a high level regardless of target nucleotide identity at a 3′position on a target RNA sequence. In some embodiments, gRNAs canperform at a high level in the absence of a G at a 3′ position on atarget ssDNA sequence. Furthermore, target DNA detected by Cas13disclosed herein can be directly from organisms, or can be indirectlygenerated by nucleic acid amplification methods, such as PCR and LAMP orany amplification method described herein. Key steps for the sensitivedetection of a target DNA, such as a target ssDNA, by a DNA-activatedprogrammable RNA nuclease, such as Cas13a, can include: (1) productionor isolation of DNA to concentrations above about 0.1 nM per reactionfor in vitro diagnostics, (2) selection of a target sequence with theappropriate sequence features to enable DNA detection as these featuresare distinct from those required for RNA detection, and (3) buffercomposition that enhances DNA detection. The detection of a target DNAby a DNA-activated programmable RNA nuclease can be connected to avariety of readouts including fluorescence, lateral flow,electrochemistry, or any other readouts described herein. Multiplexingof programmable DNA nuclease, such as a Type V CRISPR-Cas protein, witha DNA-activated programmable RNA nuclease, such as a Type VI protein,with a DNA reporter and an RNA reporter, can enable multiplexeddetection of target ssDNAs or a combination of a target dsDNA and atarget ssDNA, respectively. Multiplexing of different RNA-activatedprogrammable RNA nucleases that have distinct RNA reporter cleavagepreferences can enable additional multiplexing. Methods for thegeneration of ssDNA for DNA-activated programmable RNA nuclease-baseddiagnostics can include (1) asymmetric PCR, (2) asymmetric isothermalamplification, such as RPA, LAMP, SDA, etc. (3) NEAR for the productionof short ssDNA molecules, and (4) conversion of RNA targets into ssDNAby a reverse transcriptase followed by RNase H digestion. Thus,DNA-activated programmable RNA nuclease detection of target DNA iscompatible with the various systems, kits, compositions, reagents, andmethods disclosed herein. For example target ssDNA detection by Cas13acan be employed in a DETECTR assay disclosed herein.

A programmable nuclease can comprise a programmable nuclease capable ofbeing activated when complexed with a guide nucleic acid and targetnucleic acid. The programmable nuclease can become activated afterbinding of a guide nucleic acid with a target nucleic acid, in which theactivated programmable nuclease can cleave the target nucleic acid andcan have trans cleavage activity. Trans cleavage activity can benon-specific cleavage of nearby nucleic acids by the activatedprogrammable nuclease, such as trans cleavage of detector nucleic acidswith a detection moiety. Once the detector nucleic acid is cleaved bythe activated programmable nuclease, the detection moiety can bereleased from the detector nucleic acid and can generate a signal. Thesignal can be immobilized on a support medium for detection. The signalcan be visualized to assess whether a target nucleic acid comprises amodification.

Reporter

Reporters, which can be referred to interchangeably reporter molecules,or detector nucleic acids, described herein are compatible for use inthe devices described herein (e.g., pneumatic valve devices, slidingvalve devices, rotating valve devices, and lateral flow devices) and maybe used in conjunction with compositions disclosed herein (e.g.,programmable nucleases, guide nucleic acids, reagents for in vitrotranscription, reagents for amplification, reagents for reversetranscription, reporters, or any combination thereof) to carry outhighly efficient, rapid, and accurate reactions for detecting whether atarget nucleic acid is present in a sample (e.g., DETECTR reactions).Described herein is a reporter comprising a single stranded detectornucleic acid comprising a detection moiety, wherein the reporter iscapable of being cleaved by the activated programmable nuclease, therebygenerating a first detectable signal. As used herein, a detector nucleicacid is used interchangeably with reporter or reporter molecule. In somecases, the detector nucleic acid is a single-stranded nucleic acidcomprising deoxyribonucleotides. In other cases, the detector nucleicacid is a single-stranded nucleic acid comprising ribonucleotides. Thedetector nucleic acid can be a single-stranded nucleic acid comprisingat least one deoxyribonucleotide and at least one ribonucleotide. Insome cases, the detector nucleic acid is a single-stranded nucleic acidcomprising at least one ribonucleotide residue at an internal positionthat functions as a cleavage site. In some cases, the detector nucleicacid comprises at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 ribonucleotideresidues at an internal position. In some cases, the detector nucleicacid comprises from 2 to 10, from 3 to 9, from 4 to 8, or from 5 to 7ribonucleotide residues at an internal position. In some cases, thedetector nucleic acid comprises from 3 to 10, from 4 to 10, from 5 to10, from 6 to 10, from 7 to 10, from 8 to 10, from 9 to 10, from 2 to 8,from 3 to 8, from 5 to 8, from 6 to 8, from 7 to 8, from 2 to 5, from 3to 5, or from 4 to 5 ribonucleotide residues at an internal position.Sometimes the ribonucleotide residues are continuous. Alternatively, theribonucleotide residues are interspersed in between non-ribonucleotideresidues. In some cases, the detector nucleic acid has onlyribonucleotide residues. In some cases, the detector nucleic acid hasonly deoxyribonucleotide residues. In some cases, the detector nucleicacid comprises nucleotides resistant to cleavage by the programmablenuclease described herein. In some cases, the detector nucleic acidcomprises synthetic nucleotides. In some cases, the detector nucleicacid comprises at least one ribonucleotide residue and at least onenon-ribonucleotide residue. In some cases, the detector nucleic acid is5-20, 5-15, 5-10, 7-20, 7-15, or 7-10 nucleotides in length. In somecases, the detector nucleic acid is from 3 to 20, from 4 to 20, from 5to 20, from 6 to 20, from 7 to 20, from 8 to 20, from 9 to 20, from 10to 20, from 15 to 20, from 3 to 15, from 4 to 15, from 5 to 15, from 6to 15, from 7 to 15, from 8 to 15, from 9 to 15, from 10 to 15, from 3to 10, from 4 to 10, from 5 to 10, from 6 to 10, from 7 to 10, from 8 to10, from 9 to 10, from 3 to 8, from 4 to 8, from 5 to 8, from 6 to 8, orfrom 7 to 8 nucleotides in length. In some cases, the detector nucleicacid comprises at least one uracil ribonucleotide. In some cases, thedetector nucleic acid comprises at least two uracil ribonucleotides.Sometimes the detector nucleic acid has only uracil ribonucleotides. Insome cases, the detector nucleic acid comprises at least one adenineribonucleotide. In some cases, the detector nucleic acid comprises atleast two adenine ribonucleotide. In some cases, the detector nucleicacid has only adenine ribonucleotides. In some cases, the detectornucleic acid comprises at least one cytosine ribonucleotide. In somecases, the detector nucleic acid comprises at least two cytosineribonucleotide. In some cases, the detector nucleic acid comprises atleast one guanine ribonucleotide. In some cases, the detector nucleicacid comprises at least two guanine ribonucleotide. A detector nucleicacid can comprise only unmodified ribonucleotides, only unmodifieddeoxyribonucleotides, or a combination thereof. In some cases, thedetector nucleic acid is from 5 to 12 nucleotides in length. In somecases, the detector nucleic acid is at least 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, or 30 nucleotides in length. In some cases, the detector nucleicacid is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. Forcleavage by a programmable nuclease comprising Cas13, a detector nucleicacid can be 5, 8, or 10 nucleotides in length. For cleavage by aprogrammable nuclease comprising Cas12, a detector nucleic acid can be10 nucleotides in length.

The single stranded detector nucleic acid can comprise a detectionmoiety capable of generating a first detectable signal. Sometimes thedetector nucleic acid comprises a protein capable of generating asignal. A signal can be a calorimetric, potentiometric, amperometric,optical (e.g., fluorescent, colorometric, etc.), or piezo-electricsignal. In some cases, a detection moiety is on one side of the cleavagesite. Optionally, a quenching moiety is on the other side of thecleavage site. Sometimes the quenching moiety is a fluorescencequenching moiety. In some cases, the quenching moiety is 5′ to thecleavage site and the detection moiety is 3′ to the cleavage site. Insome cases, the detection moiety is 5′ to the cleavage site and thequenching moiety is 3′ to the cleavage site. Sometimes the quenchingmoiety is at the 5′ terminus of the detector nucleic acid. Sometimes thedetection moiety is at the 3′ terminus of the detector nucleic acid. Insome cases, the detection moiety is at the 5′ terminus of the detectornucleic acid. In some cases, the quenching moiety is at the 3′ terminusof the detector nucleic acid. In some cases, the single-strandeddetector nucleic acid is at least one population of the single-strandednucleic acid capable of generating a first detectable signal. In somecases, the single-stranded detector nucleic acid is a population of thesingle stranded nucleic acid capable of generating a first detectablesignal. Optionally, there are more than one population ofsingle-stranded detector nucleic acid. In some cases, there are 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 30, 40, 50, or greater than50, or any number spanned by the range of this list of differentpopulations of single-stranded detector nucleic acids capable ofgenerating a detectable signal. In some cases there are from 2 to 50,from 3 to 40, from 4 to 30, from 5 to 20, or from 6 to 10 differentpopulations of single-stranded detector nucleic acids capable ofgenerating a detectable signal. In some cases there are from 2 to 50,from 5 to 50, from 10 to 50, from 15 to 50, from 20 to 50, from 25 to50, from 30 to 50, from 35 to 50, from 40 to 50, from 2 to 40, from 5 to40, from 10 to 40, from 15 to 40, from 20 to 40, from 25 to 40, from 30to 40, from 35 to 40, from 2 to 30, from 5 to 30, from 10 to 30, from 15to 30, from 20 to 30, from 25 to 30, from 2 to 20, from 5 to 20, from 10to 20, from 15 to 20, from 2 to 10, or from 5 to 10 differentpopulations of single-stranded detector nucleic acids capable ofgenerating a detectable signal.

TABLE 4 Exemplary Single Stranded Detector Nucleic Acid 5′ DetectionMoiety Sequence (SEQ ID NO: ) 3′ Quencher* /56-FAM/ rUrUrUrUrU /3IABkFQ/(SEQ ID NO: 1) /5IRD700/ rUrUrUrUrU /3IRQC1N/ (SEQ ID NO: 1) /5TYE665/rUrUrUrUrU /3IAbRQSp/ (SEQ ID NO: 1) /5Alex594N/ rUrUrUrUrU /3IAbRQSp/(SEQ ID NO: 1) /5ATTO633N/ rUrUrUrUrU /3IAbRQSp/ (SEQ ID NO: 1) /56-FAM/rUrUrUrUrUrUrUrU /3IABkFQ/ (SEQ ID NO: 2) /5IRD700/ rUrUrUrUrUrUrUrU/3IRQC1N/ (SEQ ID NO: 2) /5TYE665/ rUrUrUrUrUrUrUrU /EIAbRQSp/(SEQ ID NO: 2) /5Alex594N/ rUrUrUrUrUrUrUrU /3IAbRQSp/ (SEQ ID NO: 2)/5ATTO663N/ rUrUrUrUrUrUrUrU /3IAbRQSp/ (SEQ ID NO: 2) /56-FAM/rUrUrUrUrUrUrUrUrUrU /3IABkFQ/ (SEQ ID NO: 3) /5IRD700/rUrUrUrUrUrUrUrUrUrU /3IRQC1N/ (SEQ ID NO: 3) /5TYE665/rUrUrUrUrUrUrUrUrUrU /3IAbRQSp/ (SEQ ID NO: 3) /5Alex594N/rUrUrUrUrUrUrUrUrUrU /3IAbRQSp/ (SEQ ID NO: 3) /5ATTO633N/rUrUrUrUrUrUrUrUrUrU /3IAbRQSp/ (SEQ ID NO: 3) /56-FAM/ TTTTrUrUTTTT/3IABkFQ/ (SEQ ID NO: 4) /5IRD700/ TTTTrUrUTTTT /3IRQC1N/ (SEQ ID NO: 4)/5TYE665/ TTTTrUrUTTTT /3IAbRQSp/ (SEQ ID NO: 4) /5Alex594N/TTTTrUrUTTTT /3IAbRQSp/ (SEQ ID NO: 4) /5ATTO633N/ TTTTrUrUTTTT/3IAbRQSp/ (SEQ ID NO: 4) /56-FAM/ TTrUrUTT /3IABkFQ/ (SEQ ID NO: 5)/5IRD700/ TTrUrUTT /3IRQC1N/ (SEQ ID NO: 5) /5TYE665/ TTrUrUTT/3IAbRQSp/ (SEQ ID NO: 5) /5Alex594N/ TTrUrUTT /3IAbRQSp/ (SEQ ID NO: 5)/5ATTO633N/ TTrUrUTT /3IAbRQSp/ (SEQ ID NO: 5) /56-FAM/ TArArUGC/3IABkFQ/ (SEQ ID NO: 6) /5IRD700/ TArArUGC /3IRQC1N/ (SEQ ID NO: 6)/5TYE665/ TArArUGC /3IAbRQSp/ (SEQ ID NO: 6) /5Alex594N/ TArArUGC/3IAbRQSp/ (SEQ ID NO: 6) /5ATTO633N/ TArArUGC /3IAbRQSp/ (SEQ ID NO: 6)/56-FAM/ TArUrGGC /3IABkFQ/ (SEQ ID NO: 7) /5IRD700/ TArUrGGC /3IRQC1N/(SEQ ID NO: 7) /5TYE665/ TArUrGGC /3IAbRQSp/ (SEQ ID NO: 7) /5Alex594N/TArUrGGC /3IAbRQSp/ (SEQ ID NO: 7) /5ATTO633N/ TArUrGGC /3IAbRQSp/(SEQ ID NO: 7) /56-FAM/ rUrUrUrUrU /3IABkFQ/ (SEQ ID NO: 8) /5IRD700/rUrUrUrUrU /3IRQC1N/ (SEQ ID NO: 8) /5TYE665/ rUrUrUrUrU /3IAbRQSp/(SEQ ID NO: 8) /5Alex594N/ rUrUrUrUrU /3IAbRQSp/ (SEQ ID NO: 8)/5ATTO633N/ rUrUrUrUrU /3IAbRQSp/ (SEQ ID NO: 8) /56-FAM/ TTATTATT/3IABkFQ/ (SEQ ID NO: 9) /56-FAM/ TTATTATT /3IABkFQ/ (SEQ ID NO: 9)/5IRD700/ TTATTATT /3IRQC1N/ (SEQ ID NO: 9) /5TYE665/ TTATTATT/3IAbRQSp/ (SEQ ID NO: 9) /5Alex594N/ TTATTATT /3IAbRQSp/ (SEQ ID NO: 9)/5ATTO633N/ TTATTATT /3IAbRQSp/ (SEQ ID NO: 9) /56-FAM/ TTTTTT /3IABkFQ/(SEQ ID NO: 10) /56-FAM/ TTTTTTTT /3IABkFQ/ (SEQ ID NO: 11) /56-FAM/TTTTTTTTTT /3IABkFQ/ (SEQ ID NO: 12) /56-FAM/ TTTTTTTTTTTT /3IABkFQ/(SEQ ID NO: 13) /56-FAM/ TTTTTTTTTTTTTT /3IABkFQ/ (SEQ ID NO: 14)/56-FAM/ AAAAAA /3IABkFQ/ (SEQ ID NO: 15) /56-FAM/ CCCCCC /3IABkFQ/(SEQ ID NO: 16) /56-FAM/ GGGGGG /3IABkFQ/ (SEQ ID NO: 17) /56-FAM/TTATTATT /3IABkFQ/ (SEQ ID NO: 9) /56-FAM/: 5′ 6-Fluorescein (IntegratedDNA Technologies) /3IABkFQ/: 3′ Iowa Black FQ (Integrated DNATechnologies) /5IRD700/: 5′ IRDye 700 (Integrated DNA Technologies)/5TYE665/: 5′ TYE 665 (Integrated DNA Technologies) /5Alex594N/:5′ Alexa Fluor 594 (NHS Ester) (Integrated DNA Technologies)/5ATTO633N/: 5′ ATTO TM 633 (NHS Ester) (Integrated DNA Technologies)/3IRQC1N/: 3′ IRDye QC-1 Quencher (Li-Cor) /3IAbRQSp/: 3′ Iowa Black RQ(Integrated DNA Technologies) rU: uracil ribonucleotide rG: guanineribonucleotide *This Table refers to the detection moiety and quenchermoiety as their tradenames and their source is identified. However,alternatives, generics, or non-tradename moieties with similar functionfrom other sources can also be used.

A detection moiety can be an infrared fluorophore. A detection moietycan be a fluorophore that emits fluorescence in the range of from 500 nmand 720 nm. A detection moiety can be a fluorophore that emitsfluorescence in the range of from 500 nm and 720 nm. In some cases, thedetection moiety emits fluorescence at a wavelength of 700 nm or higher.In other cases, the detection moiety emits fluorescence at about 660 nmor about 670 nm. In some cases, the detection moiety emits fluorescencein the range of from 500 to 520, 500 to 540, 500 to 590, 590 to 600, 600to 610, 610 to 620, 620 to 630, 630 to 640, 640 to 650, 650 to 660, 660to 670, 670 to 680, 680 to 690, 690 to 700, 700 to 710, 710 to 720, or720 to 730 nm. In some cases, the detection moiety emits fluorescence inthe range from 450 nm to 750 nm, from 500 nm to 750 nm, from 550 nm to750 nm, from 600 nm to 750 nm, from 650 nm to 750 nm, from 700 nm to 750nm, from 450 nm to 700 nm, from 500 nm to 700 nm, from 550 nm to 700 nm,from 600 nm to 700 nm, from 650 nm to 700 nm, from 450 nm to 650 nm,from 500 nm to 650 nm, from 550 nm to 650 nm, from 600 nm to 650 nm,from 450 nm to 600 nm, from 500 nm to 600 nm, from 550 nm to 600 nm,from 450 nm to 550 nm, from 500 nm to 550 nm, or from 450 nm to 500 nm.A detection moiety can be a fluorophore that emits a fluorescence in thesame range as 6-Fluorescein, IRDye 700, TYE 665, Alex Fluor, or ATTO TM633 (NHS Ester). A detection moiety can be fluorescein amidite,6-Fluorescein, IRDye 700, TYE 665, Alex Fluor 594, or ATTO TM 633 (NHSEster). A detection moiety can be a fluorophore that emits afluorescence in the same range as 6-Fluorescein (Integrated DNATechnologies), IRDye 700 (Integrated DNA Technologies), TYE 665(Integrated DNA Technologies), Alex Fluor 594 (Integrated DNATechnologies), or ATTO TM 633 (NHS Ester) (Integrated DNA Technologies).A detection moiety can be fluorescein amidite, 6-Fluorescein (IntegratedDNA Technologies), a digoxigenin, IRDye 700 (Integrated DNATechnologies), TYE 665 (Integrated DNA Technologies), Alex Fluor 594(Integrated DNA Technologies), or ATTO TM 633 (NHS Ester) (IntegratedDNA Technologies). Other fluorophores consistent with the presentdisclosure include ALEXA FLUOR 405, Alexa 488, Cy2, Cy3, Cy3.5, Cy5,Cy5.5, Cy7, ALEXA FLUOR 647, or other suitable fluorophores. Any of thedetection moieties described herein can be from any commerciallyavailable source, can be an alternative with a similar function, ageneric, or a non-tradename of the detection moieties listed.

A detection moiety can be chosen for use based on the type of sample tobe tested. For example, a detection moiety that is an infraredfluorophore is used with a urine sample. As another example, SEQ ID NO:1 with a fluorophore that emits a fluorescence around 520 nm is used fortesting in non-urine samples, and SEQ ID NO: 8 with a fluorophore thatemits a fluorescence around 700 nm is used for testing in urine samples.

A quenching moiety can be chosen based on its ability to quench thedetection moiety. A quenching moiety can be a non-fluorescentfluorescence quencher. A quenching moiety can quench a detection moietythat emits fluorescence in the range of from 500 nm and 720 nm. Aquenching moiety can quench a detection moiety that emits fluorescencein the range of from 500 nm and 720 nm. In some cases, the quenchingmoiety quenches a detection moiety that emits fluorescence at awavelength of 700 nm or higher. In other cases, the quenching moietyquenches a detection moiety that emits fluorescence at about 660 nm orabout 670 nm. In some cases, the quenching moiety quenches a detectionmoiety that emits fluorescence in the range of from 500 to 520, 500 to540, 500 to 590, 590 to 600, 600 to 610, 610 to 620, 620 to 630, 630 to640, 640 to 650, 650 to 660, 660 to 670, 670 to 680, 680 to 690, 690 to700, 700 to 710, 710 to 720, or 720 to 730 nm. In some cases, thequenching moiety quenches a detection moiety that emits fluoresecence inthe range from 450 nm to 750 nm, from 500 nm to 750 nm, from 550 nm to750 nm, from 600 nm to 750 nm, from 650 nm to 750 nm, from 700 nm to 750nm, from 450 nm to 700 nm, from 500 nm to 700 nm, from 550 nm to 700 nm,from 600 nm to 700 nm, from 650 nm to 700 nm, from 450 nm to 650 nm,from 500 nm to 650 nm, from 550 nm to 650 nm, from 600 nm to 650 nm,from 450 nm to 600 nm, from 500 nm to 600 nm, from 550 nm to 600 nm,from 450 nm to 550 nm, from 500 nm to 550 nm, or from 450 nm to 500 nm.A quenching moiety can quench fluorescein amidite, 6-Fluorescein, IRDye700, TYE 665, Alex Fluor 594, or ATTO TM 633 (NHS Ester). A quenchingmoiety can be Iowa Black RQ, Iowa Black FQ or IRDye QC-1 Quencher. Aquenching moiety can quench fluorescein amidite, 6-Fluorescein(Integrated DNA Technologies), IRDye 700 (Integrated DNA Technologies),TYE 665 (Integrated DNA Technologies), Alex Fluor 594 (Integrated DNATechnologies), or ATTO TM 633 (NHS Ester) (Integrated DNA Technologies).A quenching moiety can be Iowa Black RQ (Integrated DNA Technologies),Iowa Black FQ (Integrated DNA Technologies) or IRDye QC-1 Quencher(LiCor). Any of the quenching moieties described herein can be from anycommercially available source, can be an alternative with a similarfunction, a generic, or a non-tradename of the quenching moietieslisted.

The generation of the detectable signal from the release of thedetection moiety indicates that cleavage by the programmable nucleasehas occurred and that the sample contains the target nucleic acid. Insome cases, the detection moiety comprises a fluorescent dye. Sometimesthe detection moiety comprises a fluorescence resonance energy transfer(FRET) pair. In some cases, the detection moiety comprises an infrared(IR) dye. In some cases, the detection moiety comprises an ultraviolet(UV) dye. Alternatively or in combination, the detection moietycomprises a polypeptide. Sometimes the detection moiety comprises abiotin. Sometimes the detection moiety comprises at least one of avidinor streptavidin. In some instances, the detection moiety comprises apolysaccharide, a polymer, or a nanoparticle. In some instances, thedetection moiety comprises a gold nanoparticle or a latex nanoparticle.

In some embodiments, the reporter comprises a nucleic acid conjugated toan affinity molecule and the affinity molecule conjugated to thefluorophore (e.g., nucleic acid—affinity molecule—fluophore) or thenucleic acid conjugated to the fluorophore and the fluorophoreconjugated to the affinity molecule (e.g., nucleicacid—fluorophore—affinity molecule). In some embodiments, a linkerconjugates the nucleic acid to the affinity molecule. In someembodiments, a linker conjugates the affinity molecule to thefluorophore. In some embodiments, a linker conjugates the nucleic acidto the fluorophore. A linker can be any suitable linker known in theart. In some embodiments, the nucleic acid of the reporter can bedirectly conjugated to the affinity molecule and the affinity moleculecan be directly conjugated to the fluorophore or the nucleic acid can bedirectly conjugated to the fluorophore and the fluorophore can bedirectly conjugated to the affinity molecule. In this context, “directlyconjugated” indicated that no intervening molecules, polypeptides,proteins, or other moieties are present between the two moietiesdirectly conjugated to each other. For example, if a reporter comprisesa nucleic acid directly conjugated to an affinity molecule and anaffinity molecule directly conjugated to a fluorophore—no interveningmoiety is present between the nucleic acid and the affinity molecule andno intervening moiety is present between the affinity molecule and thefluorophore. The affinity molecule can be biotin, avidin, streptavidin,or any similar molecule. Additional examples of affinity molecules arebiotin, glutathione, maltose, or chitin.

A detection moiety can be any moiety capable of generating acalorimetric, potentiometric, amperometric, optical (e.g., fluorescent,colorometric, etc.), or piezo-electric signal. A detector nucleic acid,sometimes, is protein-nucleic acid that is capable of generating acalorimetric, potentiometric, amperometric, optical (e.g., fluorescent,colorometric, etc.), or piezo-electric signal upon cleavage of thenucleic acid. Often a calorimetric signal is heat produced aftercleavage of the detector nucleic acids. Sometimes, a calorimetric signalis heat absorbed after cleavage of the detector nucleic acids. Apotentiometric signal, for example, is electrical potential producedafter cleavage of the detector nucleic acids. An amperometric signal canbe movement of electrons produced after the cleavage of detector nucleicacid. Often, the signal is an optical signal, such as a colorometricsignal or a fluorescence signal. An optical signal is, for example, alight output produced after the cleavage of the detector nucleic acids.Sometimes, an optical signal is a change in light absorbance betweenbefore and after the cleavage of detector nucleic acids. Often, apiezo-electric signal is a change in mass between before and after thecleavage of the detector nucleic acid.

Often, the protein-nucleic acid is an enzyme-nucleic acid. The enzymemay be sterically hindered when present as in the enzyme-nucleic acid,but then functional upon cleavage from the nucleic acid. The enzymeproduces a reaction with a substrate. An enzyme can be invertase. Often,the substrate of invertase is sucrose and a DNS reagent can be used tomonitor invertase activity. In some cases, it is preferred that thenucleic acid (e.g., DNA) and invertase are conjugated using aheterobifunctiona linker via sulfo-SMCC chemistry.

Sometimes the protein-nucleic acid is a substrate-nucleic acid. Oftenthe substrate is a substrate that produces a reaction with an enzyme.

A protein-nucleic acid may be attached to a solid support, for exampleas part of a microfluidic or lateral flow device as disclosed herein.The solid support, for example, is a surface. A surface can be anelectrode. Sometimes the solid support is a bead. Often the bead is amagnetic bead. Upon cleavage, the protein is liberated from the solidand interacts with other mixtures. For example, the protein is anenzyme, and upon cleavage of the nucleic acid of the enzyme-nucleicacid, the enzyme flows through a chamber into a mixture comprising thesubstrate. When the enzyme meets the enzyme substrate, a reactionoccurs, such as a colorimetric reaction, which is then detected. Asanother example, the protein is an enzyme substrate, and upon cleavageof the nucleic acid of the enzyme substrate-nucleic acid, the enzymeflows through a chamber into a mixture comprising the enzyme. When theenzyme substrate meets the enzyme, a reaction occurs, such as acalorimetric reaction, which is then detected.

In some cases, the reporter comprises a substrate-nucleic acid. Thesubstrate may be sequestered from its cognate enzyme when present as inthe substrate-nucleic acid, but then is released from the nucleic acidupon cleavage, wherein the released substrate can contact the cognateenzyme to produce a detectable signal. Often, the substrate is sucroseand the cognate enzyme is invertase, and a DNS reagent can be used tomonitor invertase activity.

A major advantage of the devices and methods disclosed herein is thedesign of excess reporters to total nucleic acids in an unamplified oran amplified sample, not including the nucleic acid of the reporter.Total nucleic acids can include the target nucleic acids and non-targetnucleic acids, not including the nucleic acid of the reporter. Thenon-target nucleic acids can be from the original sample, either lysedor unlysed. The non-target nucleic acids can also be byproducts ofamplification. Thus, the non-target nucleic acids can include bothnon-target nucleic acids from the original sample, lysed or unlysed, andfrom an amplified sample. The presence of a large amount of non-targetnucleic acids, an activated programmable nuclease may be inhibited inits ability to bind and cleave the reporter sequences. This is becausethe activated programmable nucleases collaterally cleaves any nucleicacids. If total nucleic acids are in present in large amounts, they mayoutcompete reporters for the programmable nucleases. The devices andmethods disclosed herein are designed to have an excess of reporter tototal nucleic acids, such that the detectable signals from cleavagereactions (e.g., DETECTR reactions) are particularly superior. In someembodiments, the reporter can be present in at least 1.5 fold, at least2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10fold, at least 11 fold, at least 12 fold, at least 13 fold, at least 14fold, at least 15 fold, at least 16 fold, at least 17 fold, at least 18fold, at least 19 fold, at least 20 fold, at least 30 fold, at least 40fold, at least 50 fold, at least 60 fold, at least 70 fold, at least 80fold, at least 90 fold, at least 100 fold, from 1.5 fold to 100 fold,from 2 fold to 10 fold, from 10 fold to 20 fold, from 20 fold to 30fold, from 30 fold to 40 fold, from 40 fold to 50 fold, from 50 fold to60 fold, from 60 fold to 70 fold, from 70 fold to 80 fold, from 80 foldto 90 fold, from 90 fold to 100 fold, from 1.5 fold to 10 fold, from 1.5fold to 20 fold, from 10 fold to 40 fold, from 20 fold to 60 fold, orfrom 10 fold to 80 fold excess of total nucleic acids.

A second significant advantage of the devices and methods disclosedherein is the design of an excess volume comprising the guide nucleicacid, the programmable nuclease, and the reporter, which contacts asmaller volume comprising the sample with the target nucleic acid ofinterest. The smaller volume comprising the sample can be unlysedsample, lysed sample, or lysed sample which has undergone anycombination of reverse transcription, amplification, and in vitrotranscription. The presence of various reagents in a crude, non-lysedsample, a lysed sample, or a lysed and amplified sample, such as buffer,magnesium sulfate, salts, the pH, a reducing agent, primers, dNTPs,NTPs, cellular lysates, non-target nucleic acids, primers, or othercomponents, can inhibit the ability of the programmable nuclease to findand cleave the nucleic acid of the reporter. This may be due to nucleicacids that are not the reporter, which outcompete the nucleic acid ofthe reporter, for the programmable nuclease. Alternatively, variousreagents in the sample may simply inhibit the activity of theprogrammable nuclease. Thus, the devices and methods provided herein forcontacting an excess volume comprising the guide nucleic acid, theprogrammable nuclease, and the reporter to a smaller volume comprisingthe sample with the target nucleic acid of interest provides forsuperior detection of the target nucleic acid by ensuring that theprogrammable nuclease is able to find and cleaves the nucleic acid ofthe reporter. In some embodiments, the volume comprising the guidenucleic acid, the programmable nuclease, and the reporter (can bereferred to as “a second volume”) is 4-fold greater than a volumecomprising the sample (can be referred to as “a first volume”). In someembodiments, the volume comprising the guide nucleic acid, theprogrammable nuclease, and the reporter (can be referred to as “a secondvolume”) is at least 1.5 fold, at least 2 fold, at least 3 fold, atleast 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, atleast 8 fold, at least 9 fold, at least 10 fold, at least 11 fold, atleast 12 fold, at least 13 fold, at least 14 fold, at least 15 fold, atleast 16 fold, at least 17 fold, at least 18 fold, at least 19 fold, atleast 20 fold, at least 30 fold, at least 40 fold, at least 50 fold, atleast 60 fold, at least 70 fold, at least 80 fold, at least 90 fold, atleast 100 fold, from 1.5 fold to 100 fold, from 2 fold to 10 fold, from10 fold to 20 fold, from 20 fold to 30 fold, from 30 fold to 40 fold,from 40 fold to 50 fold, from 50 fold to 60 fold, from 60 fold to 70fold, from 70 fold to 80 fold, from 80 fold to 90 fold, from 90 fold to100 fold, from 1.5 fold to 10 fold, from 1.5 fold to 20 fold, from 10fold to 40 fold, from 20 fold to 60 fold, or from 10 fold to 80 foldgreater than a volume comprising the sample (can be referred to as “afirst volume”). In some embodiments, the volume comprising the sample isat least 0.5 ul, at least 1 ul, at least at least 1 uL, at least 2 uL,at least 3 uL, at least 4 uL, at least 5 uL, at least 6 uL, at least 7uL, at least 8 uL, at least 9 uL, at least 10 uL, at least 11 uL, atleast 12 uL, at least 13 uL, at least 14 uL, at least 15 uL, at least 16uL, at least 17 uL, at least 18 uL, at least 19 uL, at least 20 uL, atleast 25 uL, at least 30 uL, at least 35 uL, at least 40 uL, at least 45uL, at least 50 uL, at least 55 uL, at least 60 uL, at least 65 uL, atleast 70 uL, at least 75 uL, at least 80 uL, at least 85 uL, at least 90uL, at least 95 uL, at least 100 uL, from 0.5 uL to 5 ul uL, from 5 uLto 10 uL, from 10 uL to 15 uL, from 15 uL to 20 uL, from 20 uL to 25 uL,from 25 uL to 30 uL, from 30 uL to 35 uL, from 35 uL to 40 uL, from 40uL to 45 uL, from 45 uL to 50 uL, from 10 uL to 20 uL, from 5 uL to 20uL, from 1 uL to 40 uL, from 2 uL to 10 uL, or from 1 uL to 10 uL. Insome embodiments, the volume comprising the programmable nuclease, theguide nucleic acid, and the reporter is at least 10 uL, at least 11 uL,at least 12 uL, at least 13 uL, at least 14 uL, at least 15 uL, at least16 uL, at least 17 uL, at least 18 uL, at least 19 uL, at least 20 uL,at least 21 uL, at least 22 uL, at least 23 uL, at least 24 uL, at least25 uL, at least 26 uL, at least 27 uL, at least 28 uL, at least 29 uL,at least 30 uL, at least 40 uL, at least 50 uL, at least 60 uL, at least70 uL, at least 80 uL, at least 90 uL, at least 100 uL, at least 150 uL,at least 200 uL, at least 250 uL, at least 300 uL, at least 350 uL, atleast 400 uL, at least 450 uL, at least 500 uL, from 10 uL to 15 ul uL,from 15 uL to 20 uL, from 20 uL to 25 uL, from 25 uL to 30 uL, from 30uL to 35 uL, from 35 uL to 40 uL, from 40 uL to 45 uL, from 45 uL to 50uL, from 50 uL to 55 uL, from 55 uL to 60 uL, from 60 uL to 65 uL, from65 uL to 70 uL, from 70 uL to 75 uL, from 75 uL to 80 uL, from 80 uL to85 uL, from 85 uL to 90 uL, from 90 uL to 95 uL, from 95 uL to 100 uL,from 100 uL to 150 uL, from 150 uL to 200 uL, from 200 uL to 250 uL,from 250 uL to 300 uL, from 300 uL to 350 uL, from 350 uL to 400 uL,from 400 uL to 450 uL, from 450 uL to 500 uL, from 10 uL to 20 uL, from10 uL to 30 uL, from 25 uL to 35 uL, from 10 uL to 40 uL, from 20 uL to50 uL, from 18 uL to 28 uL, or from 17 uL to 22 uL.

A reporter may be a hybrid nucleic acid reporter. A hybrid nucleic acidreporter comprises a nucleic acid with at least one deoxyribonucleotideand at least one ribonucleotide. In some embodiments, the nucleic acidof the hybrid nucleic acid reporter can be of any length and can haveany mixture of DNAs and RNAs. For example, in some cases, longerstretches of DNA can be interrupted by a few ribonucleotides.Alternatively, longer stretches of RNA can be interrupted by a fewdeoxyribonucleotides. Alternatively, every other base in the nucleicacid may alternate between ribonucleotides and deoxyribonucleotides. Amajor advantage of the hybrid nucleic acid reporter is increasedstability as compared to a pure RNA nucleic acid reporter. For example,a hybrid nucleic acid reporter can be more stable in solution,lyophilized, or vitrified as compared to a pure DNA or pure RNAreporter.

The reporter can be lyophilized or vitrified. The reporter can besuspended in solution or immobilized on a surface. For example, thereporter can be immobilized on the surface of a chamber in a device asdisclosed herein. In some cases, the reporter is immobilized on beads,such as magnetic beads, in a chamber of a device as disclosed hereinwhere they are held in position by a magnet placed below the chamber.

Signals

The devices, systems, fluidic devices, kits, and methods for detectingthe presence of a target nucleic acid in a sample described herein maycomprise a generation of a signal in response to the presence or absenceof the target nucleic acid in the sample. The generation of a signal inresponse to the presence or absence of the target nucleic acid in thesample as described herein is compatible with the methods and devicesdescribed herein (e.g., pneumatic valve devices, sliding valve devices,rotating valve devices, and lateral flow devices) and may be result formthe use of compositions disclosed herein (e.g., programmable nucleases,guide nucleic acids, reagents for in vitro transcription, reagents foramplification, reagents for reverse transcription, reporters, or anycombination thereof) to carry out highly efficient, rapid, and accuratereactions for detecting whether a target nucleic acid is present in asample (e.g., DETECTR reactions). As disclosed herein, detecting thepresence or absence of a target nucleic acid of interest involvesmeasuring a signal emitted from a detection moiety present in areporter, after cleavage of the reporter by an activated programmablenuclease. Thus, the detecting steps disclosed herein involve measuringthe presence of a target nucleic acid, quantifying how much of thetarget nucleic acid is present, or, measuring a signal indicating thatthe target nucleic acid is absent in a sample. In some embodiments, asignal is generated upon cleavage of the detector nucleic acid by theprogrammable nuclease. In other embodiments, the signal changes uponcleavage of the detector nucleic acid by the programmable nuclease. Inother embodiments, a signal may be present in the absence of detectornucleic acid cleavage and disappear upon cleavage of the target nucleicacid by the programmable nuclease. For example, a signal may be producedin a microfluidic device or lateral flow device after contacting asample with a composition comprising a programmable nuclease.

Often, the signal is a colorimetric signal or a signal visible by eye.In some instances, the signal is fluorescent, electrical, chemical,electrochemical, or magnetic. A signal can be a calorimetric,potentiometric, amperometric, optical (e.g., fluorescent, colorometric,etc.), or piezo-electric signal. In some cases, the detectable signal isa colorimetric signal or a signal visible by eye. In some instances, thedetectable signal is fluorescent, electrical, chemical, electrochemical,or magnetic. In some cases, the first detection signal is generated bybinding of the detection moiety to the capture molecule in the detectionregion, where the first detection signal indicates that the samplecontained the target nucleic acid. Sometimes the system is capable ofdetecting more than one type of target nucleic acid, wherein the systemcomprises more than one type of guide nucleic acid and more than onetype of detector nucleic acid. In some cases, the detectable signal isgenerated directly by the cleavage event. Alternatively or incombination, the detectable signal is generated indirectly by the signalevent. Sometimes the detectable signal is not a fluorescent signal. Insome instances, the detectable signal is a colorimetric or color-basedsignal. In some cases, the detected target nucleic acid is identifiedbased on its spatial location on the detection region of the supportmedium. In some cases, the second detectable signal is generated in aspatially distinct location than the first generated signal.

Buffers

The reagents described herein can also include buffers, which arecompatible with the devices, systems, fluidic devices, kits, and methodsdisclosed herein. The buffers described herein are compatible for use inthe devices described herein (e.g., pneumatic valve devices, slidingvalve devices, rotating valve devices, and lateral flow devices) and maybe used in conjunction with compositions disclosed herein (e.g.,programmable nucleases, guide nucleic acids, reagents for in vitrotranscription, reagents for amplification, reagents for reversetranscription, reporters, or any combination thereof) to carry outhighly efficient, rapid, and accurate reactions for detecting whetherthe target nucleic acid is in the sample (e.g., DETECTR reactions).These buffers are compatible with the other reagents, samples, andsupport mediums as described herein for detection of an ailment, such asa disease, cancer, or genetic disorder, or genetic information, such asfor phenotyping, genotyping, or determining ancestry. The methodsdescribed herein can also include the use of buffers, which arecompatible with the methods disclosed herein. For example, a buffercomprises 20 mM HEPES pH 6.8, 50 mM KCl, 5 mM MgCl₂, and 5% glycerol. Insome instances the buffer comprises from 0 to 100, 0 to 75, 0 to 50, 0to 25, 0 to 20, 0 to 10, 0 to 5, 5 to 10, 5 to 15, 5 to 20, 5 to 25, to30, 5 to 40, 5 to 50, 5 to 75, 5 to 100, 10 to 20, 10 to 30, 10 to 40,10 to 50, 15 to 20, 15 to 25, 15 to 30, 15 to 4, 15 to 50, 20 to 25, 20to 30, 20 to 40, or 20 to 50 mM HEPES pH 6.8. The buffer can comprise to0 to 500, 0 to 400, 0 to 300, 0 to 250, 0 to 200, 0 to 150, 0to 100, 0to 75, 0 to 50, 0 to 25, 0 to 20, 0 to 10, 0 to 5, 5 to 10, 5 to 15, 5to 20, 5 to 25, to 30, 5 to 40, 5 to 50, 5 to 75, 5 to 100, 5 to 150, 5to 200, 5 to 250, 5 to 300, 5 to 400, 5 to 500, 25 to 50, 25 to 75, 25to 100, 50 to 100, 50 150, 50 to 200, 50 to 250, 50 to 300, 100 to 200,100 to 250, 100 to 300, or 150 to 250 mM KCl. In other instances thebuffer comprises 0 to 100, 0 to 75, 0 to 50, 0 to 25, 0 to 20, 0 to 10,0 to 5, 5 to 10, 5 to 15, 5 to 20, 5 to 25, to 30, 5 to 40, 5 to 50, 5to 75, 5 to 100, 10 to 20, 10 to 30, 10 to 40, 10 to 50, 15 to 20, 15 to25, 15 to 30, 15 to 4, 15 to 50, 20 to 25, 20 to 30, 20 to 40, or 20 to50 mM MgCl₂. The buffer can comprise 0 to 25, 0 to 20, 0 to 10, 0 to 5,5 to 10, 5 to 15, 5 to 20, 5 to 25, 5 to 30% glycerol. The buffer cancomprise from 0% to 30%, from 5% to 30%, from 10% to 30%, from 15% to30%, from 20% to 30%, from 25% to 30%, from 0% to 25%, from 2% to 25%,from 5% to 25%, from 10% to 25%, from 15% to 25%, from 20% to 25%, from0% to 20%, from 5% to 20%, from 10% to 20%, from 15% to 20%, from 0% to15%, from 5% to 15%, from 10% to 15%, from 0% to 10%, from 5% to 10%, orfrom 0% to 5% glycerol.

As another example, a buffer comprises 100 mM Imidazole pH 7.5; 250 mMKCl, 25 mM MgCl₂, 50 ug/mL BSA, 0.05% Igepal Ca-630, and 25% Glycerol.In some instances the buffer comprises 0 to 500, 0 to 400, 0 to 300, 0to 250, 0 to 200, 0 to 150, 0 to 100, 0 to 75, 0 to 50, 0 to 25, 0 to20, 0 to 10, 0 to 5, 5 to 10, 5 to 15, 5 to 20, 5 to 25, to 30, 5 to 40,5 to 50, 5 to 75, 5 to 100, 5 to 150, 5 to 200, 5 to 250, 5 to 300, 5 to400, 5 to 500, 25 to 50, 25 to 75, 25 to 100, 50 to 100, 50 150, 50 to200, 50 to 250, 50 to 300, 100 to 200, 100 to 250, 100 to 300, or 150 to250 mM Imidazole pH 7.5. In some instances the buffer comprises from 50mM to 500 mM, from 150 mM to 500 mM, from 200 mM to 500 mM, from 250 mMto 500 mM, from 300 mM to 500 mM, from 350 mM to 500 mM, from 400 mM to500 mM, from 450 mM to 500 mM, from 0 mM to 450 mM, from 50 mM to 450mM, from 150 mM to 450 mM, from 200 mM to 450 mM, from 250 mM to 450 mM,from 300 mM to 450 mM, from 350 mM to 450 mM, from 400 mM to 450 mM,from 0 mM to 400 mM, from 50 mM to 400 mM, from 150 mM to 400 mM, from200 mM to 400 mM, from 250 mM to 400 mM, from 300 mM to 400 mM, from 350mM to 400 mM, from 0 mM to 350 mM, from 50 mM to 350 mM, from 150 mM to350 mM, from 200 mM to 350 mM, from 250 mM to 350 mM, from 300 mM to 350mM, from 0 mM to 300 mM, from 50 mM to 300 mM, from 150 mM to 300 mM,from 200 mM to 300 mM, from 250 mM to 300 mM, from 50 mM to 250 mM, from150 mM to 250 mM, from 200 mM to 250 mM, from 50 mM to 200 mM, from 150mM to 200 mM, from 50 mM to 150 mM, from 100 mM to 150 mM, from 50 mM to100 mM Imdazole pH 7.5. The buffer can comprise 0 to 500, 0 to 400, 0 to300, 0 to 250, 0 to 200, 0 to 150, 0 to 100, 0 to 75, 0 to 50, 0 to 25,0 to 20, 0 to 10, 0 to 5, 5 to 10, 5 to 15, 5 to 20, 5 to 25, to 30, 5to 40, 5 to 50, 5 to 75, 5 to 100, 5 to 150, 5 to 200, 5 to 250, 5 to300, 5 to 400, 5 to 500, 25 to 50, 25 to 75, 25 to 100, 50 to 100, 50150, 50 to 200, 50 to 250, 50 to 300, 100 to 200, 100 to 250, 100 to300, or 150 to 250 mM KCl. In other instances the buffer comprises 0 to100, 0 to 75, 0 to 50, 0 to 25, 0 to 20, 0 to 10, 0 to 5, 5 to 10, 5 to15, 5 to 20, 5 to 25, to 30, 5 to 40, 5 to 50, 5 to 75, 5 to 100, 10 to20, 10 to 30, 10 to 40, 10 to 50, 15 to 20, 15 to 25, 15 to 30, 15 to 4,15 to 50, 20 to 25, 20 to 30, 20 to 40, or 20 to 50 mM MgCl₂. Thebuffer, in some instances, comprises 0 to 100, 0 to 75, 0 to 50, 0 to25, 0 to 20, 0 to 10, 0 to 5, 5 to 50, 5 to 75, 5 to 100, 10 to 20, 10to 50, 10 to 75, 10 to 100, 25 to 50, 25 to 75 25 to 100, 50 to 75, or50 to 100 ug/mL BSA. In some instances, the buffer comprises 0 to 1, 0to 0.5, 0 to 0.25, 0 to 0.01, 0 to 0.05, 0 to 0.025, 0 to 0.01, 0.01 to0.025, 0.01 to 0.05, 0.01 to 0.1, 0.01 to 0.25, 0.01, to 0.5, 0.01 to 1,0.025 to 0.05, 0.025 to 0.1, 0.025, to 0.5, 0.025 to 1, 0.05 to 0.1,0.05 to 0.25, 0.05 to 0.5, 0.05 to 0.75, 0.05 to 1, 0.1 to 0.25, 0.1 to0.5, or 0.1 to 1% Igepal Ca-630. The buffer can comprise 0 to 25, 0 to20, 0 to 10, 0 to 5, 5 to 10, 5 to 15, 5 to 20, 5 to 25, 5 to 30%glycerol. The buffer can comprise from 0% to 30%, from 5% to 30%, from10% to 30%, from 15% to 30%, from 20% to 30%, from 25% to 30%, from 0%to 25%, from 2% to 25%, from 5% to 25%, from 10% to 25%, from 15% to25%, from 20% to 25%, from 0% to 20%, from 5% to 20%, from 10% to 20%,from 15% to 20%, from 0% to 15%, from 5% to 15%, from 10% to 15%, from0% to 10%, from 5% to 10%, or from 0% to 5% glycerol.

Stability

The reagents, compositions, and kits disclosed herein may comprisestable compositions and reagents. These stable compositions and reagentsas described herein are compatible with the methods and devicesdescribed herein (e.g., pneumatic valve devices, sliding valve devices,rotating valve devices, and lateral flow devices) and may becompositions disclosed herein (e.g., programmable nucleases, guidenucleic acids, reagents for in vitro transcription, reagents foramplification, reagents for reverse transcription, reporters, or anycombination thereof) to carry out highly efficient, rapid, and accuratereactions for detecting whether a target nucleic acid is present in asample (e.g., DETECTR reactions). Disclosed herein are stablecompositions of the reagents and the programmable nuclease system foruse in the methods as discussed herein. The reagents and programmablenuclease system described herein may be stable in various storageconditions including refrigerated, ambient, and accelerated conditions.Disclosed herein are stable reagents. The stability may be measured forthe reagents and programmable nuclease system themselves or the reagentsand programmable nuclease system present on the support medium.

In some instances, stable as used herein refers to a reagents havingabout 5% w/w or less total impurities at the end of a given storageperiod. Stability may be assessed by HPLC or any other known testingmethod. The stable reagents may have about 10% w/w, about 5% w/w, about4% w/w, about 3% w/w, about 2% w/w, about 1% w/w, or about 0.5% w/wtotal impurities at the end of a given storage period. The stablereagents may have from 0.5% w/w to 10% w/w, from 1% w/w to 8% w/w, from2% w/w to 7% w/w, or from 3% w/w to 5% w/w total impurities at the endof a given storage period.

In some embodiments, stable as used herein refers to a reagents andprogrammable nuclease system having about 10% or less loss of detectionactivity at the end of a given storage period and at a given storagecondition. Detection activity can be assessed by known positive sampleusing a known method. Alternatively or combination, detection activitycan be assessed by the sensitivity, accuracy, or specificity. In someembodiments, the stable reagents has about 10%, about 9%, about 8%,about 7%, about 6%, about 5%, about 4%, about 3%, about 2%, about 1%, orabout 0.5% loss of detection activity at the end of a given storageperiod. In some embodiments, the stable reagents has from 0.5% to 10%,from from 1% to 8%, from 2% to 7%, or from 3% to 5% loss of detectionactivity at the end of a given storage period.

In some embodiments, the stable composition has zero loss of detectionactivity at the end of a given storage period and at a given storagecondition. The given storage condition may comprise humidity of equal toor less than 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%relative humidity. The controlled storage environment may comprisehumidity from 0% to 50% relative humidity, from 0% to 40% relativehumidity, from 0% to 30% relative humidity, from 0% to 20% relativehumidity, or from 0% to 10% relative humidity. The controlled storageenvironment may comprise humidity from 10% to 80%, from 10% to 70%, from10% to 60%, from 20% to 50%, from 20% to 40%, or from 20% to 30%relative humidity. The controlled storage environment may comprisetemperatures of about −100° C., about −80° C., about −20° C., about 4°C., about 25° C. (room temperature), or about 40° C. The controlledstorage environment may comprise temperatures from −80° C. to 25° C., orfrom −100° C. to 40° C. The controlled storage environment may comprisetemperatures from −20° C. to 40° C., from −20° C. to 4° C., or from 4°C. to 40° C. The controlled storage environment may protect the systemor kit from light or from mechanical damage. The controlled storageenvironment may be sterile or aseptic or maintain the sterility of thelight conduit. The controlled storage environment may be aseptic orsterile.

Multiplexing

The devices, systems, fluidic devices, kits, and methods describedherein can be multiplexed in a number of ways. These methods ofmultiplexing are, for example, consistent with fluidic devices disclosedherein for detection of a target nucleic acid within the sample, whereinthe fluidic device may comprise multiple pumps, valves, reservoirs, andchambers for sample preparation, amplification of a target nucleic acidwithin the sample, mixing with a programmable nuclease, and detection ofa detectable signal arising from cleavage of detector nucleic acids bythe programmable nuclease within the fluidic system itself.

Methods consistent with the present disclosure include a multiplexingmethod of assaying for a target nucleic acid in a sample. A multiplexingmethod comprises contacting the sample to a complex comprising a guidenucleic acid comprising a segment that is reverse complementary to asegment of the target nucleic acid and a programmable nuclease thatexhibits sequence independent cleavage upon forming a complex comprisingthe segment of the guide nucleic acid binding to the segment of thetarget nucleic acid; and assaying for a signal indicating cleavage of atleast some protein-nucleic acids of a population of protein-nucleicacids, wherein the signal indicates a presence of the target nucleicacid in the sample and wherein absence of the signal indicates anabsence of the target nucleic acid in the sample. As another example,multiplexing method of assaying for a target nucleic acid in a sample,for example, comprises: a) contacting the sample to a complex comprisinga guide nucleic acid comprising a segment that is reverse complementaryto a segment of the target nucleic acid and a programmable nuclease thatexhibits sequence independent cleavage upon forming a complex comprisingthe segment of the guide nucleic acid binding to the segment of thetarget nucleic acid; b) contacting the complex to a substrate; c)contacting the substrate to a reagent that differentially reacts with acleaved substrate; and d) assaying for a signal indicating cleavage ofthe substrate, wherein the signal indicates a presence of the targetnucleic acid in the sample and wherein absence of the signal indicatesan absence of the target nucleic acid in the sample. Often, thesubstrate is an enzyme-nucleic acid. Sometimes, the substrate is anenzyme substrate-nucleic acid.

Multiplexing can be either spatial multiplexing wherein multipledifferent target nucleic acids at the same time, but the reactions arespatially separated. Often, the multiple target nucleic acids aredetected using the same programmable nuclease, but different guidenucleic acids. The multiple target nucleic acids sometimes are detectedusing the different programmable nucleases. In the case wherein multipletarget nucleic acids are detected using the different programmablenucleases, the method involves using a first programmable nuclease,which upon activation (e.g., after binding of a first guide nucleic acidto a first target), cleaves a nucleic acid of a first reporter and asecond programmable nuclease, which upon activation (e.g., after bindingof a second guide nucleic acid to a second target), cleaves a nucleicacid of a second reporter. For example, the first programmable nucleasecan be a Cas13 nuclease, which upon activation, cleaves an RNA of afirst reporter and the second programmable nuclease can be a Cas12nuclease, which upon activation, cleaves a DNA of a second reporter. Insome embodiments, a pair of orthogonal Cas13a proteins can be used. Forexample, a first Cas13a protein in the orthogonal pair has a preferencefor cleaving a first nucleotide-rich nucleic acid in a first reporterand a second Cas13a protein in the orthogonal pair has a preference forcleaving a second nucleotide-rich nucleic acid in a second reporter,wherein the first nucleotide and the second nucleotide are different.One example of an orthogonal pair is LbaCas13a, which has a preferencefor cleaving an A-rich nucleic acid, and LbuCas13a, which has apreference for cleaving a U-rich nucleic acid. Orthogonal pairs ofCas13s can be LbaCas13a (A) and HheCas13a (U), LbaCas13a (A) andRcaCas13a (U), LbaCas13a (A) and PprCas13a (U), LbaCas13a (A) andLneCas13a (U), LbaCas13a (A) and LbuCas13a (U), LbaCas13a (A) andLwaCas13a (U), LbaCas13a (A) and LshCas13a (U), EreCas13a (A) andHheCas13a (U), EreCas13a (A) and RcaCas13a (U), EreCas13a (A) andPprCas13a (U), EreCas13a (A) and LneCas13a (U), EreCas13a (A) andLbuCas13a (U), EreCas13a (A) and LwaCas13a (U), EreCas13a (A) andLshCas13a (U), EreCas13a (A) and LseCas13a (U), CamCas13a (A) andHheCas13a (U), CamCas13a (A) and RcaCas13a (U), CamCas13a (A) andPprCas13a (U), CamCas13a (A) and LneCas13a (U), CamCas13a (A) andLbuCas13a (U), CamCas13a (A) and LwaCas13a (U), CamCas13a (A) andLshCas13a (U), CamCas13a (A) and LseCas13a (U), wherein the preferenceof nucleotide in the nucleic acid of the reporter is specified inparentheses. Sometimes, multiplexing can be single reaction multiplexingwherein multiple different target acids are detected in a singlereaction volume. Often, at least two different programmable nucleasesare used in single reaction multiplexing. For example, multiplexing canbe enabled by immobilization of multiple categories of detector nucleicacids within a fluidic system, to enable detection of multiple targetnucleic acids within a single fluidic system. Multiplexing allows fordetection of multiple target nucleic acids in one kit or system. In somecases, the multiple target nucleic acids comprise different targetnucleic acids to a virus, a bacterium, or a pathogen responsible for onedisease. In some cases, the multiple target nucleic acids comprisedifferent target nucleic acids associated with a cancer or geneticdisorder. Multiplexing for one disease, cancer, or genetic disorderincreases at least one of sensitivity, specificity, or accuracy of theassay to detect the presence of the disease in the sample. In somecases, the multiple target nucleic acids comprise target nucleic acidsdirected to different viruses, bacteria, or pathogens responsible formore than one disease. In some cases, multiplexing allows fordiscrimination between multiple target nucleic acids, such as targetnucleic acids that comprise different genotypes of the same bacteria orpathogen responsible for a disease, for example, for a wild-typegenotype of a bacteria or pathogen and for genotype of a bacteria orpathogen comprising a mutation, such as a single nucleotide polymorphism(SNP) that can confer resistance to a treatment, such as antibiotictreatment. Multiplexing, thus, allows for multiplexed detection ofmultiple genomic alleles. For example, multiplexing comprises method ofassaying comprising a single assay for a microorganism species using afirst programmable nuclease and an antibiotic resistance pattern in amicroorganism using a second programmable nuclease. Sometimes,multiplexing allows for discrimination between multiple target nucleicacids of different HPV strains, for example, HPV16 and HPV18. In somecases, the multiple target nucleic acids comprise target nucleic acidsdirected to different cancers or genetic disorders. Often, multiplexingallows for discrimination between multiple target nucleic acids, such astarget nucleic acids that comprise different genotypes, for example, fora wild-type genotype and for SNP genotype. Multiplexing for multiplediseases, cancers, or genetic disorders provides the capability to testa panel of diseases from a single sample. For example, multiplexing formultiple diseases can be valuable in a broad panel testing of a newpatient or in epidemiological surveys. Often multiplexing is used foridentifying bacterial pathogens in sepsis or other diseases associatedwith multiple pathogens.

Furthermore, signals from multiplexing can be quantified. For example, amethod of quantification for a disease panel comprises assaying for aplurality of unique target nucleic acids in a plurality of aliquots froma sample, assaying for a control nucleic acid control in a secondaliquot of the sample, and quantifying a plurality of signals of theplurality of unique target nucleic acids by measuring signals producedby cleavage of detector nucleic acids compared to the signal produced inthe second aliquot. In this context, a unique target nucleic acid refersto the sequence of a nucleic acid that has an at least one nucleotidedifference from the sequences of the other nucleic acids in theplurality. Multiple copies of each target nucleic acid may be present.For example, a unique target nucleic population may comprise multiplecopies of the unique target nucleic acid. Often the plurality of uniquetarget nucleic acids are from a plurality of bacterial pathogens in thesample. Sometimes the quantification of a signal of the pluralitycorrelates with a concentration of a unique target nucleic acid of theplurality for the unique target nucleic acid of the plurality thatproduced the signal of the plurality. The disease panel can be for anycommunicable disease, such as sepsis.

The devices, systems, fluidic devices, kits, and methods describedherein can be multiplexed by various configurations of the reagents andthe support medium. In some cases, the kit or system is designed to havemultiple support mediums encased in a single housing. Sometimes, themultiple support mediums housed in a single housing share a singlesample pad. The single sample pad may be connected to the supportmediums in various designs such as a branching or a radial formation.Alternatively, each of the multiple support mediums has its own samplepad. In some cases, the kit or system is designed to have a singlesupport medium encased in a housing, where the support medium comprisesmultiple detection spots for detecting multiple target nucleic acids.Sometimes, the reagents for multiplexed assays comprise multiple guidenucleic acids, multiple programmable nucleases, and multiple singlestranded detector nucleic acids, where a combination of one of the guidenucleic acids, one of the programmable nucleases, and one of the singlestranded detector nucleic acids detects one target nucleic acid and canprovide a detection spot on the detection region. In some cases, thecombination of a guide nucleic acid, a programmable nuclease, and asingle stranded detector nucleic acid configured to detect one targetnucleic acid is mixed with at least one other combination in a singlereagent chamber. In some cases, the combination of a guide nucleic acid,a programmable nuclease, and a single stranded detector nucleic acidconfigured to detect one target nucleic acid is mixed with at least oneother combination on a single support medium. When these combinations ofreagents are contacted with the sample, the reaction for the multipletarget nucleic acids occurs simultaneously in the same medium or reagentchamber. Sometimes, this reacted sample is applied to the multiplexedsupport medium described herein.

In some cases, the combination of a guide nucleic acid, a programmablenuclease, and a single stranded detector nucleic acid configured todetect one target nucleic acid is provided in its own reagent chamber orits own support medium. In this case, multiple reagent chambers orsupport mediums are provided in the device, kit, or system, where onereagent chamber is designed to detect one target nucleic acid. In thiscase, multiple support mediums are used to detect the panel of diseases,cancers, or genetic disorders of interest.

In some instances, the multiplexed devices, systems, fluidic devices,kits, and methods detect at least 2 different target nucleic acids in asingle reaction. In some instances, the multiplexed devices, systems,fluidic devices, kits, and methods detect at least 3 different targetnucleic acids in a single reaction. In some instances, the multiplexeddevices, systems, fluidic devices, kits, and methods detect at least 4different target nucleic acids in a single reaction. In some instances,the multiplexed devices, systems, fluidic devices, kits, and methodsdetect at least 5 different target nucleic acids in a single reaction.In some cases, the multiplexed devices, systems, fluidic devices, kits,and methods detect at least 6, 7, 8, 9, or 10 different target nucleicacids in a single reaction. In some instances, the multiplexed kitsdetect at least 2 different target nucleic acids in a single kit. Insome instances, the multiplexed kits detect at least 3 different targetnucleic acids in a single kit. In some instances, the multiplexed kitsdetect at least 4 different target nucleic acids in a single kit. Insome instances, the multiplexed kits detect at least 5 different targetnucleic acids in a single kit. In some instances, the multiplexed kitsdetect at least 6, 7, 8, 9, or 10 different target nucleic acids in asingle kit. In some instances, the multiplexed kits detect from 2 to 10,from 3 to 10, from 4 to 10, from 5 to 10, from 6 to 10, from 7 to 10,from 8 to 10, from 9 to 10, from 2 to 9, from 3 to 9, from 4 to 9, from5 to 9, from 6 to 9, from 7 to 9, from 8 to 9, from 2 to 8, from 3 to 8,from 4 to 8, from 5 to 8, from 6 to 8, from 7 to 8, from 2 to 7, from 3to 7, from 4 to 7, from 5 to 7, from 6 to 7, from 2 to 6, from 3 to 6,from 4 to 6, from 5 to 6, from 2 to 5, from 3 to 5, from 4 to 5, from 2to 4, from 3 to 4, or from 2 to 3 different target nucleic acids in asingle kit. Multiplexing can be carried out in a single-pot or “one-pot”reaction, where reverse transcription, amplification, in vitrotranscription, or any combination thereof, and detection are carried outin a single volume. Multiplexing can be carried out in a “two-potreaction”, where reverse transcription, amplification, in vitrotranscription, or any combination thereof, are carried out in a firstvolume and detection is carried out in a second volume.

Detection Methods

The devices, systems, fluidic devices, kits, and methods describedherein may comprise a generation of a signal in response to the presenceor absence of a target nucleic acid in a sample which may be detectedusing detection methods described herein. The present disclosureprovides methods of assaying for a target nucleic acid as describedherein wherein a signal is detected. For example, a method of assayingfor a target nucleic acid in a sample comprises contacting the sample toa complex comprising a guide nucleic acid comprising a segment that isreverse complementary to a segment of the target nucleic acid and aprogrammable nuclease that exhibits sequence independent cleavage uponforming a complex comprising the segment of the guide nucleic acidbinding to the segment of the target nucleic acid; and assaying for asignal indicating cleavage of at least some protein-nucleic acids of apopulation of protein-nucleic acids, wherein the signal indicates apresence of the target nucleic acid in the sample and wherein absence ofthe signal or a presence of the signal near background indicates anabsence of the target nucleic acid in the sample. As another example, amethod of assaying for a target nucleic acid in a sample, for example,comprises: a) contacting the sample to a complex comprising a guidenucleic acid comprising a segment that is reverse complementary to asegment of the target nucleic acid and a programmable nuclease thatexhibits sequence independent cleavage upon forming a complex comprisingthe segment of the guide nucleic acid binding to the segment of thetarget nucleic acid; b) contacting the complex to a substrate; c)contacting the substrate to a reagent that differentially reacts with acleaved substrate; and d) assaying for a signal indicating cleavage ofthe substrate, wherein the signal indicates a presence of the targetnucleic acid in the sample and wherein absence of the signal or apresence of the signal near background indicates an absence of thetarget nucleic acid in the sample. Often, the substrate is anenzyme-nucleic acid. Sometimes, the substrate is an enzymesubstrate-nucleic acid.

In some cases, the threshold of detection, for a subject method ofdetecting a single stranded target nucleic acid in a sample, is lessthan or equal to 10 nM. The term “threshold of detection” is used hereinto describe the minimal amount of target nucleic acid that must bepresent in a sample in order for detection to occur. For example, when athreshold of detection is 10 nM, then a signal can be detected when atarget nucleic acid is present in the sample at a concentration of 10 nMor more. In some cases, the threshold of detection is less than or equalto 5 nM, 1 nM, 0.5 nM, 0.1 nM, 0.05 nM, 0.01 nM, 0.005 nM, 0.001 nM,0.0005 nM, 0.0001 nM, 0.00005 nM, 0.00001 nM, 10 pM, 1 pM, 500 fM, 250fM, 100 fM, 50 fM, 10 fM, 5 fM, 1 fM, 500 attomolar (aM), 100 aM, 50 aM,10 aM, or 1 aM. In some cases, the threshold of detection is in a rangeof from 1 aM to 1 nM, 1 aM to 500 pM, 1 aM to 200 pM, 1 aM to 100 pM, 1aM to 10 pM, 1 aM to 1 pM, 1 aM to 500 fM, 1 aM to 100 fM, 1 aM to 1 fM,1 aM to 500 aM, 1 aM to 100 aM, 1 aM to 50 aM, 1 aM to 10 aM, 10 aM to 1nM, 10 aM to 500 pM, 10 aM to 200 pM, 10 aM to 100 pM, 10 aM to 10 pM,10 aM to 1 pM, 10 aM to 500 fM, 10 aM to 100 fM, 10 aM to 1 fM, 10 aM to500 aM, 10 aM to 100 aM, 10 aM to 50 aM, 100 aM to 1 nM, 100 aM to 500pM, 100 aM to 200 pM, 100 aM to 100 pM, 100 aM to 10 pM, 100 aM to 1 pM,100 aM to 500 fM, 100 aM to 100 fM, 100 aM to 1 fM, 100 aM to 500 aM,500 aM to 1 nM, 500 aM to 500 pM, 500 aM to 200 pM, 500 aM to 100 pM,500 aM to 10 pM, 500 aM to 1 pM, 500 aM to 500 fM, 500 aM to 100 fM, 500aM to 1 fM, 1 fM to 1 nM, 1 fM to 500 pM, 1 fM to 200 pM, 1 fM to 100pM, 1 fM to 10 pM, 1 fM to 1 pM, 10 fM to 1 nM, 10 fM to 500 pM, 10 fMto 200 pM, 10 fM to 100 pM, 10 fM to 10 pM, 10 fM to 1 pM, 500 fM to 1nM, 500 fM to 500 pM, 500 fM to 200 pM, 500 fM to 100 pM, 500 fM to 10pM, 500 fM to 1 pM, 800 fM to 1 nM, 800 fM to 500 pM, 800 fM to 200 pM,800 fM to 100 pM, 800 fM to 10 pM, 800 fM to 1 pM, from 1 pM to 1 nM, 1pM to 500 pM, 1 pM to 200 pM, 1 pM to 100 pM, or 1 pM to 10 pM. In somecases, the threshold of detection in a range of from 800 fM to 100 pM, 1pM to 10 pM, 10 fM to 500 fM, 10 fM to 50 fM, 50 fM to 100 fM, 100 fM to250 fM, or 250 fM to 500 fM. In some cases the threshold of detection isin a range of from 2 aM to 100 pM, from 20 aM to 50 pM, from 50 aM to 20pM, from 200 aM to 5 pM, or from 500 aM to 2 pM. In some cases thethreshold of detection is in a range of from 1 aM to 2 nM, from 10 aM to2 nM, from 100 aM to 2 nM, from 1 fM to 2 nM, from 10 fM to 2 nM, from100 fM to 2 nM, from 1 pM to 2 nM, from 10 pM to 2 nM, from 100 pM to 2nM, from 1 aM to 200 pM, from 10 aM to 200 pM, from 100 aM to 200 pM,from 1 fM to 200 pM, from 10 fM to 200 pM, from 100 fM to 200 pM, from 1pM to 200 pM, from 10 pM to 200 pM, from 1 aM to 20 pM, from 10 aM to 20pM, from 100 aM to 20 pM, from 1 fM to 20 pM, from 10 fM to 20 pM, from100 fM to 20 pM, from 1 pM to 20 pM, from 1 aM to 2 pM, from 10 aM to 2pM, from 100 aM to 2 pM, from 1 fM to 2 pM, from 10 fM to 2 pM, from 100fM to 2 pM, from 1 aM to 200 fM, from 10 aM to 200 fM, from 100 aM to200 fM, from 1 fM to 200 fM, from 10 fM to 200 fM, from 1 aM to 20 fM,from 10 aM to 20 fM, from 100 aM to 20 fM, from 1 fM to 20 fM, from 1 aMto 2 fM, from 10 aM to 2 fM, from 100 aM to 2 fM, from 1 aM to 200 aM,from 10 aM to 200 aM, or from 1 aM to 20 aM. In some cases, the minimumconcentration at which a single stranded target nucleic acid is detectedin a sample is in a range of from 1 aM to 1 nM, 10 aM to 1 nM, 100 aM to1 nM, 500 aM to 1 nM, 1 fM to 1 nM, 1 fM to 500 pM, 1 fM to 200 pM, 1 fMto 100 pM, 1 fM to 10 pM, 1 fM to 1 pM, 10 fM to 1 nM, 10 fM to 500 pM,10 fM to 200 pM, 10 fM to 100 pM, 10 fM to 10 pM, 10 fM to 1 pM, 500 fMto 1 nM, 500 fM to 500 pM, 500 fM to 200 pM, 500 fM to 100 pM, 500 fM to10 pM, 500 fM to 1 pM, 800 fM to 1 nM, 800 fM to 500 pM, 800 fM to 200pM, 800 fM to 100 pM, 800 fM to 10 pM, 800 fM to 1 pM, 1 pM to 1 nM, 1pM to 500 pM, from 1 pM to 200 pM, 1 pM to 100 pM, or 1 pM to 10 pM. Insome cases, the minimum concentration at which a single stranded targetnucleic acid is detected in a sample is in a range of from 2 aM to 100pM, from 20 aM to 50 pM, from 50 aM to 20 pM, from 200 aM to 5 pM, orfrom 500 aM to 2 pM. In some cases, the minimum concentration at which asingle stranded target nucleic acid is detected in a sample is in arange of from 1 aM to 2 nM, from 10 aM to 2 nM, from 100 aM to 2 nM,from 1 fM to 2 nM, from 10 fM to 2 nM, from 100 fM to 2 nM, from 1 pM to2 nM, from 10 pM to 2 nM, from 100 pM to 2 nM, from 1 aM to 200 pM, from10 aM to 200 pM, from 100 aM to 200 pM, from 1 fM to 200 pM, from 10 fMto 200 pM, from 100 fM to 200 pM, from 1 pM to 200 pM, from 10 pM to 200pM, from 1 aM to 20 pM, from 10 aM to 20 pM, from 100 aM to 20 pM, from1 fM to 20 pM, from 10 fM to 20 pM, from 100 fM to 20 pM, from 1 pM to20 pM, from 1 aM to 2 pM, from 10 aM to 2 pM, from 100 aM to 2 pM, from1 fM to 2 pM, from 10 fM to 2 pM, from 100 fM to 2 pM, from 1 aM to 200fM, from 10 aM to 200 fM, from 100 aM to 200 fM, from 1 fM to 200 fM,from 10 fM to 200 fM, from 1 aM to 20 fM, from 10 aM to 20 fM, from 100aM to 20 fM, from 1 fM to 20 fM, from 1 aM to 2 fM, from 10 aM to 2 fM,from 100 aM to 2 fM, from 1 aM to 200 aM, from 10 aM to 200 aM, or from1 aM to 20 aM. In some cases, the minimum concentration at which asingle stranded target nucleic acid can be detected in a sample is in arange of from 1 aM to 100 pM. In some cases, the minimum concentrationat which a single stranded target nucleic acid can be detected in asample is in a range of from 1 fM to 100 pM. In some cases, the minimumconcentration at which a single stranded target nucleic acid can bedetected in a sample is in a range of from 10 fM to 100 pM. In somecases, the minimum concentration at which a single stranded targetnucleic acid can be detected in a sample is in a range of from 800 fM to100 pM. In some cases, the minimum concentration at which a singlestranded target nucleic acid can be detected in a sample is in a rangeof from 1 pM to 10 pM. In some cases, the devices, systems, fluidicdevices, kits, and methods described herein detect a targetsingle-stranded nucleic acid in a sample comprising a plurality ofnucleic acids such as a plurality of non-target nucleic acids, where thetarget single-stranded nucleic acid is present at a concentration as lowas 1 aM, 10 aM, 100 aM, 500 aM, 1 fM, 10 fM, 500 fM, 800 fM, 1 pM, 10pM, 100 pM, or 1 pM.

When a guide nucleic acid binds to a target nucleic acid, theprogrammable nuclease's trans cleavage activity can be initiated, anddetector nucleic acids can be cleaved, resulting in the detection offluorescence. Some methods as described herein can a method of assayingfor a target nucleic acid in a sample comprises contacting the sample toa complex comprising a guide nucleic acid comprising a segment that isreverse complementary to a segment of the target nucleic acid and aprogrammable nuclease that exhibits sequence independent cleavage uponforming a complex comprising the segment of the guide nucleic acidbinding to the segment of the target nucleic acid; and assaying for asignal indicating cleavage of at least some protein-nucleic acids of apopulation of protein-nucleic acids, wherein the signal indicates apresence of the target nucleic acid in the sample and wherein absence ofthe signal or a presence of the signal near background indicates anabsence of the target nucleic acid in the sample. The cleaving of thedetector nucleic acid using the programmable nuclease may cleave with anefficiency of 50% as measured by a change in a signal that iscalorimetric, potentiometric, amperometric, optical (e.g., fluorescent,colorometric, etc.), or piezo-electric, as non-limiting examples. Somemethods as described herein can be a method of detecting a targetnucleic acid in a sample comprising contacting the sample comprising thetarget nucleic acid with a guide nucleic acid targeting a target nucleicacid segment, a programmable nuclease capable of being activated whencomplexed with the guide nucleic acid and the target nucleic acidsegment, a single stranded detector nucleic acid comprising a detectionmoiety, wherein the detector nucleic acid is capable of being cleaved bythe activated programmable nuclease, thereby generating a firstdetectable signal, cleaving the single stranded detector nucleic acidusing the programmable nuclease that cleaves as measured by a change incolor, and measuring the first detectable signal on the support medium.The cleaving of the single stranded detector nucleic acid using theprogrammable nuclease may cleave with an efficiency of 50% as measuredby a change in color. In some cases, the cleavage efficiency is at least40%, 50%, 60%, 70%, 80%, 90%, or 95% as measured by a change in color.In some embodiments, the cleavage efficiency is from 40% to 95%, from50% to 95%, from 60% to 95%, from 65% to 95%, from 75% to 95%, from 80%to 95%, from 90% to 95%, from 40% to 90%, from 50% to 90%, from 60% to90%, from 65% to 90%, from 75% to 90%, from 80% to 90%, from 40% to 80%,from 50% to 80%, from 60% to 80%, from 65% to 80%, from 75% to 80%, from40% to 75%, from 50% to 75%, from 60% to 75%, from 65% to 75%, from 40%to 60%, from 50% to 60%, or from 40% to 50% as measured by a change incolor. The change in color may be a detectable colorimetric signal or asignal visible by eye. The change in color may be measured as a firstdetectable signal. The first detectable signal can be detectable within5 minutes of contacting the sample comprising the target nucleic acidwith a guide nucleic acid targeting a target nucleic acid segment, aprogrammable nuclease capable of being activated when complexed with theguide nucleic acid and the target nucleic acid segment, and a singlestranded detector nucleic acid comprising a detection moiety, whereinthe detector nucleic acid is capable of being cleaved by the activatednuclease. The first detectable signal can be detectable within 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50,55, 60, 70, 80, 90, 100, 110, or 120 minutes of contacting the sample.In some embodiments, the first detectable signal can be detectablewithin from 1 to 120, from 5 to 100, from 10 to 90, from 15 to 80, from20 to 60, or from 30 to 45 minutes of contacting the sample. In someembodiments, the first detectable signal can be detectable within from15 minutes to 120 minutes, from 30 minutes to 120 minutes, from 45minutes to 120 minutes, from 60 minutes to 120 minutes, from 75 minutesto 120 minutes, from 90 minutes to 120 minutes, from 105 minutes to 120minutes, from 5 minutes to 90 minutes, from 15 minutes to 90 minutes,from 30 minutes to 90 minutes, from 45 minutes to 90 minutes, from 60minutes to 90 minutes, from 75 minutes to 90 minutes, from 5 minutes to75 minutes, from 15 minutes to 75 minutes, from 30 minutes to 75minutes, from 45 minutes to 75 minutes, from 60 minutes to 75 minutes,from 5 minutes to 60 minutes, from 15 minutes to 60 minutes, from 30minutes to 60 minutes, from 45 minutes to 60 minutes, from 5 minutes to45 minutes, from 15 minutes to 45 minutes, from 30 minutes to 45minutes, from 5 minutes to 30 minutes, from 15 minutes to 30 minutes, orfrom 5 minutes to 15 minutes.

In some cases, the devices, systems, fluidic devices, kits, and methodsdescribed herein detect a target single-stranded nucleic acid in asample where the sample is contacted with the reagents for apredetermined length of time sufficient for the trans cleavage to occuror cleavage reaction to reach completion. In some cases, the devices,systems, fluidic devices, kits, and methods described herein detect atarget single-stranded nucleic acid in a sample where the sample iscontacted with the reagents for no greater than 60 minutes. Sometimesthe sample is contacted with the reagents for no greater than 120minutes, 110 minutes, 100 minutes, 90 minutes, 80 minutes, 70 minutes,60 minutes, 55 minutes, 50 minutes, 45 minutes, 40 minutes, 35 minutes,30 minutes, 25 minutes, 20 minutes, 15 minutes, 10 minutes, 5 minutes, 4minutes, 3 minutes, 2 minutes, or 1 minute. Sometimes the sample iscontacted with the reagents for at least 120 minutes, 110 minutes, 100minutes, 90 minutes, 80 minutes, 70 minutes, 60 minutes, 55 minutes, 50minutes, 45 minutes, 40 minutes, 35 minutes, 30 minutes, 25 minutes, 20minutes, 15 minutes, 10 minutes, or 5 minutes. In some cases, the sampleis contacted with the reagents for from 5 minutes to 120 minutes, from 5minutes to 100 minutes, from 10 minutes to 90 minutes, from 15 minutesto 45 minutes, or from 20 minutes to 35 minutes. In some cases, thesample is contacted with the reagents for from 15 minutes to 120minutes, from 30 minutes to 120 minutes, from 45 minutes to 120 minutes,from 60 minutes to 120 minutes, from 75 minutes to 120 minutes, from 90minutes to 120 minutes, from 105 minutes to 120 minutes, from 5 minutesto 90 minutes, from 15 minutes to 90 minutes, from 30 minutes to 90minutes, from 45 minutes to 90 minutes, from 60 minutes to 90 minutes,from 75 minutes to 90 minutes, from 5 minutes to 75 minutes, from 15minutes to 75 minutes, from 30 minutes to 75 minutes, from 45 minutes to75 minutes, from 60 minutes to 75 minutes, from 5 minutes to 60 minutes,from 15 minutes to 60 minutes, from 30 minutes to 60 minutes, from 45minutes to 60 minutes, from 5 minutes to 45 minutes, from 15 minutes to45 minutes, from 30 minutes to 45 minutes, from 5 minutes to 30 minutes,from 15 minutes to 30 minutes, or from 5 minutes to 15 minutes. In somecases, the devices, systems, fluidic devices, kits, and methodsdescribed herein can detect a target nucleic acid in a sample in lessthan 10 hours, less than 9 hours, less than 8 hours, less than 7 hours,less than 6 hours, less than 5 hours, less than 4 hours, less than 3hours, less than 2 hours, less than 1 hour, less than 50 minutes, lessthan 45 minutes, less than 40 minutes, less than 35 minutes, less than30 minutes, less than 25 minutes, less than 20 minutes, less than 15minutes, less than 10 minutes, less than 9 minutes, less than 8 minutes,less than 7 minutes, less than 6 minutes, or less than 5 minutes. Insome cases, the devices, systems, fluidic devices, kits, and methodsdescribed herein can detect a target nucleic acid in a sample in from 5minutes to 10 hours, from 10 minutes to 8 hours, from 15 minutes to 6hours, from 20 minutes to 5 hours, from 30 minutes to 10 hours, from 1hour to 10 hours, from 2 hours to 10 hours, from 4 hours to 10 hours,from 5 hours to 10 hours, from 6 hours to 10 hours, from 8 hours to 10hours, from 30 minutes to 8 hours, from 1 hour to 8 hours, from 2 hoursto 8 hours, from 4 hours to 8 hours, from 5 hours to 8 hours, from 6hours to 8 hours, from 30 minutes to 6 hours, from 1 hour to 6 hours,from 2 hours to 6 hours, from 4 hours to 6 hours, from 5 hours to 6hours, from 30 minutes to 5 hours, from 1 hours to 5 hours, from 2 hoursto 5 hours, from 4 hours to 5 hours, from 30 minutes to 4 hours, from 1hour to 4 hours, from 2 hours to 4 hours, from 30 minutes to 2 hours,from 1 hour to 2 hours, from 5 minutes to 1 hour, from 15 minutes to 1hour, from 30 minutes to 1 hour, or from 45 minutes to 1 hour.

In some cases, the devices, systems, fluidic devices, kits, and methodsdescribed herein detect a target single-stranded nucleic acid with aprogrammable nuclease and a single-stranded detector nucleic acid in asample where the sample is contacted with the reagents for apredetermined length of time sufficient for trans cleavage of the singlestranded detector nucleic acid. For example, a programmable nuclease isLbuCas13a that detects a target nucleic acid and a single strandeddetector nucleic acid comprises two adjacent uracil nucleotides with agreen detectable moiety that is detected upon cleavage. As anotherexample, a programmable nuclease is LbaCas13a that detects a targetnucleic acid and a single-stranded detector nucleic acid comprises twoadjacent adenine nucleotides with a red detectable moiety that isdetected upon cleavage.

In some cases, the devices, systems, fluidic devices, kits, and methodsdescribed herein detect different two target single-stranded nucleicacids with two different programmable nucleases and two differentsingle-stranded detector nucleic acids in a sample where the sample iscontacted with the reagents for a predetermined length of timesufficient for trans cleavage of the at least two single-strandeddetector nucleic acids. For example, a first programmable nuclease isLbuCas13a, which is activated by a first single-stranded target nucleicacid and upon activation, cleaves a first single-stranded detectornucleic acid comprising two adjacent uracil nucleotides with a greendetectable moiety that is detected upon cleavage, and a secondprogrammable nuclease is LbaCas13a, which is activated by a secondsingle-stranded target nucleic acid and upon activation, cleaves asecond single-stranded detector nucleic acid comprising two adjacentadenine nucleotides with a red detectable moiety that is detected uponcleavage. In some cases, the activation of both programmable nucleasesto cleave their respective single-stranded nucleic acids, for exampleLbuCas13a that cleaves a first single-stranded detector nucleic acidcomprising two adjacent uracil nucleotides with a green detectablemoiety that is detected upon cleavage and LbaCas13a that cleaves asecond single-stranded detector nucleic acid comprises two adjacentadenine nucleotides with a red detectable moiety that is detected uponcleavage, the subsequence detection of a yellow signal indicates thatthe first single-stranded target nucleic acid and the secondsingle-stranded target nucleic are present in the sample.

Alternatively, the devices, systems, fluidic devices, kits, and methodsdescribed herein can comprise a first programmable nuclease that detectsthe presence of a first single-stranded target nucleic acid in a sampleand a second programmable nuclease that is used as a control. Forexample, a first programmable nuclease is Lbu13a, which cleaves a firstsingle-stranded detector nucleic acid comprising two adjacent uracilnucleotides with a green detectable moiety that is detected uponcleavage and which is activated by a first single-stranded targetnucleic acid if it is present in the sample, and a second programmablenuclease is Lba13a, which cleaves a second single-stranded detectornucleic acid comprising two adjacent adenine nucleotides with a reddetectable moiety that is detected upon cleavage and which is activatedby a second single-stranded target nucleic acid that is not found (andwould not be expected to ever be found) in the sample and serves as acontrol. In this case, the detection of a red signal or a yellow signalindicates there is a problem with the test (e.g., the sample contains ahigh level of other RNAses that are cleaving the single-strandeddetector nucleic acids in the absence of activation of the secondprogrammable nuclease), but the detection of a green signal indicatesthe test is working correctly and the first target single-strandednucleic acid of the first programmable nuclease is present in thesample.

As additional examples, the devices, systems, fluidic devices, kits, andmethods described herein detect different two target single-strandednucleic acids with two different programmable nucleases and twodifferent single stranded detector nucleic acids in a sample where thesample is contacted with the reagents for a predetermined length of timesufficient for trans cleavage of the at least two single strandeddetector nucleic acid. For example, a first programmable nuclease is aCas13a protein, which cleaves a first single-stranded detector nucleicthat is detected upon cleavage and which is activated by a firstsingle-stranded target nucleic acid from a sepsis RNA biomarker if it ispresent in the sample, and a second programmable nuclease is a Cas14protein, which cleaves a second single-stranded detector nucleic acidthat is detected upon cleavage and which is activated by a secondsingle-stranded target nucleic acid from a sepsis-causing bacteria.

A number of detection devices and methods are consistent with methodsdisclosed herein. For example, any device that can measure or detect acalorimetric, potentiometric, amperometric, optical (e.g., fluorescent,colorometric, etc.), or piezo-electric signal. Often a calorimetricsignal is heat produced after cleavage of the detector nucleic acids.Sometimes, a calorimetric signal is heat absorbed after cleavage of thedetector nucleic acids. A potentiometric signal, for example, iselectrical potential produced after cleavage of the detector nucleicacids. An amperometric signal can be movement of electrons producedafter the cleavage of detector nucleic acid. Often, the signal is anoptical signal, such as a colorometric signal or a fluorescence signal.An optical signal is, for example, a light output produced after thecleavage of the detector nucleic acids. Sometimes, an optical signal isa change in light absorbance between before and after the cleavage ofdetector nucleic acids. Often, a piezo-electric signal is a change inmass between before and after the cleavage of the detector nucleic acid.Sometimes, the detector nucleic acid is protein-nucleic acid. Often, theprotein-nucleic acid is an enzyme-nucleic acid.

The results from the detection region from a completed assay can bedetected and analyzed in various ways, for example, by a glucometer. Insome cases, the positive control spot and the detection spot in thedetection region is visible by eye, and the results can be read by theuser. In some cases, the positive control spot and the detection spot inthe detection region is visualized by an imaging device or other devicedepending on the type of signal. Often, the imaging device is a digitalcamera, such a digital camera on a mobile device. The mobile device mayhave a software program or a mobile application that can capture animage of the support medium, identify the assay being performed, detectthe detection region and the detection spot, provide image properties ofthe detection spot, analyze the image properties of the detection spot,and provide a result. Alternatively or in combination, the imagingdevice can capture fluorescence, ultraviolet (UV), infrared (IR), orvisible wavelength signals. The imaging device may have an excitationsource to provide the excitation energy and captures the emittedsignals. In some cases, the excitation source can be a camera flash andoptionally a filter. In some cases, the imaging device is used togetherwith an imaging box that is placed over the support medium to create adark room to improve imaging. The imaging box can be a cardboard boxthat the imaging device can fit into before imaging. In some instances,the imaging box has optical lenses, mirrors, filters, or other opticalelements to aid in generating a more focused excitation signal or tocapture a more focused emission signal. Often, the imaging box and theimaging device are small, handheld, and portable to facilitate thetransport and use of the assay in remote or low resource settings.

The assay described herein can be visualized and analyzed by a mobileapplication (app) or a software program. Using the graphic userinterface (GUI) of the app or program, an individual can take an imageof the support medium, including the detection region, barcode,reference color scale, and fiduciary markers on the housing, using acamera on a mobile device. The program or app reads the barcode oridentifiable label for the test type, locate the fiduciary marker toorient the sample, and read the detectable signals, compare against thereference color grid, and determine the presence or absence of thetarget nucleic acid, which indicates the presence of the gene, virus, orthe agent responsible for the disease, cancer, or genetic disorder. Themobile application can present the results of the test to theindividual. The mobile application can store the test results in themobile application. The mobile application can communicate with a remotedevice and transfer the data of the test results. The test results canbe viewable remotely from the remote device by another individual,including a healthcare professional. A remote user can access theresults and use the information to recommend action for treatment,intervention, clean up of an environment.

Target Nucleic Acid Detection

The methods described herein may be used to assay for or detect thepresence of a specific target nucleic acid in a sample. In someembodiments, the target nucleic acid may comprise a mutation relative toa wild type or normal genotype. The mutation may be associated with adisease phenotype, a genetic disorder, or a predisposition to a disease(e.g., cancer). The mutation may be a single nucleotide mutation, or themutation may comprise multiple nucleotides. The mutation may comprise aninsertion or a deletion of one or more nucleotides. In some embodiments,the target nucleic acid may comprise a nucleic acid from a pathogen. Thepathogen may be associated with a disease or infection. The pathogen maybe a virus, a bacterium, a protozoan, a parasite, or a fungus. Thetarget nucleic acid may be associated with a disease trait (e.g.,antibiotic resistance).

Detection of a Mutation in a Target Nucleic Acid

Disclosed herein are methods of assaying for a target nucleic acid asdescribed herein that can be used for detection of a mutation in atarget nucleic acid. For example, a method of assaying for a targetnucleic acid in a sample comprises contacting the sample to a complexcomprising a guide nucleic acid comprising a segment that is reversecomplementary to a segment of the target nucleic acid and a programmablenuclease that exhibits sequence independent cleavage upon forming acomplex comprising the segment of the guide nucleic acid binding to thesegment of the target nucleic acid; and assaying for a signal indicatingcleavage of at least some protein-nucleic acids of a population ofprotein-nucleic acids, wherein the signal indicates a presence of thetarget nucleic acid in the sample and wherein absence of the signal or apresence of the signal near background indicates an absence of thetarget nucleic acid in the sample. The detection of the signal canindicate the presence of the target nucleic acid. Sometimes, the targetnucleic acid comprises a mutation. Often, the mutation is a singlenucleotide mutation. As another example, a method of assaying for atarget nucleic acid in a sample, for example, comprises: a) contactingthe sample to a complex comprising a guide nucleic acid comprising asegment that is reverse complementary to a segment of the target nucleicacid and a programmable nuclease that exhibits sequence independentcleavage upon forming a complex comprising the segment of the guidenucleic acid binding to the segment of the target nucleic acid; b)contacting the complex to a substrate; c) contacting the substrate to areagent that differentially reacts with a cleaved substrate; and d)assaying for a signal indicating cleavage of the substrate, wherein thesignal indicates a presence of the target nucleic acid in the sample andwherein absence of the signal or a presence of the signal nearbackground indicates an absence of the target nucleic acid in thesample. Often, the substrate is an enzyme-nucleic acid. Sometimes, thesubstrate is an enzyme substrate-nucleic acid.

Methods described herein can be used to identify a mutation in a targetnucleic acid. The methods can be used to identify a single nucleotidemutation of a target nucleic acid that affects the expression of a gene.A mutation that affects the expression of gene can be a singlenucleotide mutation of a target nucleic acid within the gene, a singlenucleotide mutation of a target nucleic acid comprising RNA associatedwith the expression of a gene, or a target nucleic acid comprising asingle nucleotide mutation of a nucleic acid associated with regulationof expression of a gene, such as an RNA or a promoter, enhancer, orrepressor of the gene. Often, a status of a mutation is used to diagnoseor identify diseases associated with the mutation of target nucleicacid. Detection of target nucleic acids having a mutation are applicableto a number of fields, such as clinically, as a diagnostic, inlaboratories as a research tool, and in agricultural applications.Often, the mutation is a single nucleotide mutation.

Disease Detection

Disclosed herein are methods of assaying for a target nucleic acid asdescribed herein that can be used for disease detection. For example, amethod of assaying for a target nucleic acid in a sample comprisescontacting the sample to a complex comprising a guide nucleic acidcomprising a segment that is reverse complementary to a segment of thetarget nucleic acid and a programmable nuclease that exhibits sequenceindependent cleavage upon forming a complex comprising the segment ofthe guide nucleic acid binding to the segment of the target nucleicacid; and assaying for a signal indicating cleavage of at least someprotein-nucleic acids of a population of protein-nucleic acids, whereinthe signal indicates a presence of the target nucleic acid in the sampleand wherein absence of the signal or a presence of the signal nearbackground indicates an absence of the target nucleic acid in thesample. The detection of the signal can indicate the presence of thetarget nucleic acid. Sometimes, the target nucleic acid comprises amutation. Often, the mutation is a single nucleotide mutation. Asanother example, a method of assaying for a target nucleic acid in asample, for example, comprises: a) contacting the sample to a complexcomprising a guide nucleic acid comprising a segment that is reversecomplementary to a segment of the target nucleic acid and a programmablenuclease that exhibits sequence independent cleavage upon forming acomplex comprising the segment of the guide nucleic acid binding to thesegment of the target nucleic acid; b) contacting the complex to asubstrate; c) contacting the substrate to a reagent that differentiallyreacts with a cleaved substrate; and d) assaying for a signal indicatingcleavage of the substrate, wherein the signal indicates a presence ofthe target nucleic acid in the sample and wherein absence of the signalor a presence of the signal near background indicates an absence of thetarget nucleic acid in the sample. Often, the substrate is anenzyme-nucleic acid. Sometimes, the substrate is an enzymesubstrate-nucleic acid.

The methods as described herein can be used to identify or diagnose acancer or genetic disorder associated with a mutation in a targetnucleic acid. The methods can be used to identify a mutation of a targetnucleic acid that affects the expression of a cancer gene. A cancer genecan be any gene whose aberrant expression is associated with cancer,such as overexpression of an oncogene, suppression of tumor suppressorgene, or disregulation of a checkpoint inhibitor gene or gene associatedwith cellular growth, cellular metabolism, or the cell cycle. A mutationthat affects the expression of cancer gene can be a mutation of a targetnucleic acid within the cancer gene, a mutation of a target nucleic acidcomprising RNA associated with the expression of a cancer gene, or atarget nucleic acid comprising a mutation of a nucleic acid associatedwith regulation of expression of a cancer gene, such as an RNA or apromoter, enhancer, or repressor of the cancer gene. For example, atarget nucleic acid comprising a mutation that affects a cancer gene cancontribute to or lead to colon cancer, bladder cancer, stomach cancer,breast cancer, non-small-cell lung cancer, pancreatic cancer, esophagealcancer, cervical cancer, ovarian cancer, hepatocellular cancer, andacute myeloid leukemia. The target nucleic acid comprise a mutation of acancer gene or RNA expressed from a cancer gene. Often, the mutation isa single nucleotide mutation.

The methods can be used to identify a mutation that affects theexpression of a gene associated with a genetic disorder. A geneassociated with a genetic disorder can be a gene whose overexpression isassociated with a genetic disorder, from a gene associated with abnormalcellular growth resulting in a genetic disorder, or from a geneassociated with abnormal cellular metabolism resulting in a geneticdisorder. A mutation that affects the expression of a gene associatedwith a genetic disorder can be mutation within the gene associated witha genetic disorder, a mutation of RNA associated with a gene of thegenetic disorder, or a mutation of a nucleic acid associated withregulation of expression of a gene associated with a genetic disorder,such as an RNA or a promoter, enhancer, or repressor of the geneassociated with the genetic disorder. Often, the mutation is a singlenucleotide mutation.

Methods described herein can be used to identify a mutation in a targetnucleic acid from a bacteria, virus, or microbe. The methods can be usedto identify a mutation of a target nucleic acid that affects theexpression of a gene. A mutation that affects the expression of gene canbe a mutation of a target nucleic acid within the gene, a mutation of atarget nucleic acid comprising RNA associated with the expression of agene, or a target nucleic acid comprising a mutation of a nucleic acidassociated with regulation of expression of a gene, such as an RNA or apromoter, enhancer, or repressor of the gene. Sometimes, a status of atarget nucleic acid mutation is used to determine a pathogenicity of abacteria, virus, or microbe or treatment resistance, such as resistanceto antibiotic treatment. Often, a status of a mutation is used todiagnose or identify diseases associated with the mutation of targetnucleic acids in the bacteria, virus, or microbe. Often, the mutation isa single nucleotide mutation.

The presence or absence of a target nucleic acid may be identified in asample, for example a biological sample. In some embodiments, thebiological sample is blood, serum, plasma, saliva, urine, mucosalsample, peritoneal sample, cerebrospinal fluid, gastric secretions,nasal secretions, sputum, pharyngeal exudates, urethral or vaginalsecretions, an exudate, an effusion, or tissue. The presence or absenceof the target nucleic acid may be identified using any of the methodsdescribed herein. The presence or absence of the target nucleic acid maybe identified using any of the devices described herein. Once thepresence or absence of a target nucleic acid has been identified in thesample, a treatment may be administered to a subject, for example thesubject from whom the sample was collected. Administering treatment tothe subject may comprise administering a therapy (e.g., radiationtherapy, chemotherapy, antibiotics, antivirals, or antifungals). Thetreatment may be administered parenterally, topically, or locally. Thetreatment may be a treatment for a disease associated with a targetnucleic acid identified in the sample. In some embodiments, the subjectshows symptoms associated with a disease. In other embodiments, thesubject is asymptomatic.

Detection as a Research Tool, Point-of-Care, or Over-the-Counter

Disclosed herein are methods of assaying for a target nucleic acid asdescribed herein that can be used as a research tool, and can beprovided as reagent kits. For example, a method of assaying for a targetnucleic acid in a sample comprises contacting the sample to a complexcomprising a guide nucleic acid comprising a segment that is reversecomplementary to a segment of the target nucleic acid and a programmablenuclease that exhibits sequence independent cleavage upon forming acomplex comprising the segment of the guide nucleic acid binding to thesegment of the target nucleic acid; and assaying for a signal indicatingcleavage of at least some protein-nucleic acids of a population ofprotein-nucleic acids, wherein the signal indicates a presence of thetarget nucleic acid in the sample and wherein absence of the signal or apresence of the signal near background indicates an absence of thetarget nucleic acid in the sample. The detection of the signal canindicate the presence of the target nucleic acid. Sometimes, the targetnucleic acid comprises a mutation. Often, the mutation is a singlenucleotide mutation. As another example, a method of assaying for atarget nucleic acid in a sample, for example, comprises: a) contactingthe sample to a complex comprising a guide nucleic acid comprising asegment that is reverse complementary to a segment of the target nucleicacid and a programmable nuclease that exhibits sequence independentcleavage upon forming a complex comprising the segment of the guidenucleic acid binding to the segment of the target nucleic acid; b)contacting the complex to a substrate; c) contacting the substrate to areagent that differentially reacts with a cleaved substrate; and d)assaying for a signal indicating cleavage of the substrate, wherein thesignal indicates a presence of the target nucleic acid in the sample andwherein absence of the signal or a presence of the signal nearbackground indicates an absence of the target nucleic acid in thesample. Often, the substrate is an enzyme-nucleic acid. Sometimes, thesubstrate is an enzyme substrate-nucleic acid.

The methods as described herein can be used to identify a singlenucleotide mutation in a target nucleic acid. The methods can be used toidentify mutation of a target nucleic acid that affects the expressionof a gene. A mutation that affects the expression of gene can be asingle nucleotide mutation of a target nucleic acid within the gene, amutation of a target nucleic acid comprising RNA associated with theexpression of a gene, or a target nucleic acid comprising a mutation ofa nucleic acid associated with regulation of expression of a gene, suchas an RNA or a promoter, enhancer, or repressor of the gene. Often, themutation is a single nucleotide mutation.

The reagent kits or research tools can be used to detect any number oftarget nucleic acids, mutations, or other indications disclosed hereinin a laboratory setting. Reagent kits can be provided as reagent packsfor open box instrumentation.

In other embodiments, any of the systems, assay formats, Cas reporters,programmable nucleases, or other reagents can be used in a point-of-care(POC) test, which can be carried out at a decentralized location such asa hospital, POL, or clinic. These point-of-care tests can be used todiagnose any of the indications disclosed herein, such as influenza orstreptococcal infections, or can be used to measure the presence orabsence of a particular mutation in a target nucleic acid (e.g., EGFR).POC tests can be provided as small instruments with a consumable testcard, wherein the test card is any of the assay formats (e.g., a lateralflow assay) disclosed herein.

In still other embodiments, any of the systems, assay formats, Casreporters, programmable nucleases, or other reagents can be used in anover-the-counter (OTC), readerless format, which can be used at remotesites or at home to diagnose a range of indications. These indicationscan include influenza, streptococcal infections, or CT/NG infections.OTC products can include a consumable test card, wherein the test cardis any of the assay formats (e.g., a lateral flow assay) disclosedherein. In an OTC product, the test card can be interpreted visually orusing a mobile phone.

Detection for Agricultural Applications

Disclosed herein are methods of assaying for a target nucleic acid asdescribed herein that can be used for agricultural applications. Forexample, a method of assaying for a target nucleic acid in a samplecomprises contacting the sample to a complex comprising a guide nucleicacid comprising a segment that is reverse complementary to a segment ofthe target nucleic acid and a programmable nuclease that exhibitssequence independent cleavage upon forming a complex comprising thesegment of the guide nucleic acid binding to the segment of the targetnucleic acid; and assaying for a signal indicating cleavage of at leastsome protein-nucleic acids of a population of protein-nucleic acids,wherein the signal indicates a presence of the target nucleic acid inthe sample and wherein absence of the signal or a presence of the signalnear background indicates an absence of the target nucleic acid in thesample. The detection of the signal can indicate the presence of thetarget nucleic acid. Sometimes, the target nucleic acid comprises amutation. Often, the mutation is a single nucleotide mutation. Asanother example, a method of assaying for a target nucleic acid in asample, for example, comprises: a) contacting the sample to a complexcomprising a guide nucleic acid comprising a segment that is reversecomplementary to a segment of the target nucleic acid and a programmablenuclease that exhibits sequence independent cleavage upon forming acomplex comprising the segment of the guide nucleic acid binding to thesegment of the target nucleic acid; b) contacting the complex to asubstrate; c) contacting the substrate to a reagent that differentiallyreacts with a cleaved substrate; and d) assaying for a signal indicatingcleavage of the substrate, wherein the signal indicates a presence ofthe target nucleic acid in the sample and wherein absence of the signalor a presence of the signal near background indicates an absence of thetarget nucleic acid in the sample. Often, the substrate is anenzyme-nucleic acid. Sometimes, the substrate is an enzymesubstrate-nucleic acid.

The methods as described herein can be used to identify a mutation in atarget nucleic acid of a plant or of a bacteria, virus, or microbeassociated with a plant or soil. The methods can be used to identify amutation of a target nucleic acid that affects the expression of a gene.A mutation that affects the expression of gene can be a mutation of atarget nucleic acid within the gene, a mutation of a target nucleic acidcomprising RNA associated with the expression of a gene, or a targetnucleic acid comprising a mutation of a nucleic acid associated withregulation of expression of a gene, such as an RNA or a promoter,enhancer, or repressor of the gene. Often, the mutation is a singlenucleotide mutation.

Detection of a Target Nucleic Acid in a Fluidic Device

Disclosed herein are various fluidic devices for detection of a targetnucleic acid of interest in a biological sample. The fluidic devicesdescribed in detail below can be used to monitor the reaction of targetnucleic acids in samples with a programmable nuclease, thereby allowingfor the detection of said target nucleic acid. All samples and reagentsdisclosed herein are compatible for use with a fluidic device disclosedbelow. Any programmable nuclease, such as any Cas nuclease describedherein, are compatible for use with a fluidic device disclosed below.Support mediums and housing disclosed herein are also compatible for usein conjunction with the fluidic devices disclosed below. Multiplexingdetection, as described throughout the present disclosure, can becarried out within the fluidic devices disclosed herein. Compositionsand methods for detection and visualization disclosed herein are alsocompatible for use within the below described fluidic systems.

In the below described fluidic systems, any programmable nuclease (e.g.,CRISPR-Cas) reaction can be monitored. For example, any programmablenuclease disclosed herein can be used to cleave the reporter moleculesto generate a detection signal. In some cases, the programmable nucleaseis Cas13. Sometimes the Cas13 is Cas13a, Cas13b, Cas13c, Cas13d, orCas13e. In some cases, the programmable nuclease is Mad7 or Mad2. Insome cases, the programmable nuclease is Cas12. Sometimes the Cas12 isCas12a, Cas12b, Cas12c, Cas12d, or Cas12e. In some cases, theprogrammable nuclease is Csm1, Cas9, C2c4, C2c8, C2c5, C2c10, C2c9, orCasZ. Sometimes, the Csm1 is also called smCms1, miCms1, obCms1, orsuCms1. Sometimes Cas13a is also called C2c2. Sometimes CasZ is alsocalled Cas14a, Cas14b, Cas14c, Cas14d, Cas14e, Cas14f, Cas14g, orCas14h. Sometimes, the programmable nuclease is a type V CRISPR-Cassystem. In some cases, the programmable nuclease is a type VI CRISPR-Cassystem. Sometimes the programmable nuclease is a type III CRISPR-Cassystem. In some cases, the programmable nuclease is from at least one ofLeptotrichia shahii (Lsh), Listeria seeligeri (Lse), Leptotrichiabuccalis (Lbu), Leptotrichia wadeu (Lwa), Rhodobacter capsulatus (Rca),Herbinix hemicellulosilytica (Hhe), Paludibacter propionicigenes (Ppr),Lachnospiraceae bacterium (Lba), [Eubacterium] rectale (Ere), Listerianewyorkensis (Lny), Clostridium aminophilum (Cam), Prevotella sp. (Psm),Capnocytophaga canimorsus (Cca, Lachnospiraceae bacterium (Lba),Bergeyella zoohelcum (Bzo), Prevotella intermedia (Pin), Prevotellabuccae (Pbu), Alistipes sp. (Asp), Riemerella anatipestifer (Ran),Prevotella aurantiaca (Pau), Prevotella saccharolytica (Psa), Prevotellaintermedia (Pin2), Capnocytophaga canimorsus (Cca), Porphyromonas gulae(Pgu), Prevotella sp. (Psp), Porphyromonas gingivalis (Pig), Prevotellaintermedia (Pin3), Enterococcus italicus (Ei), Lactobacillus salivarius(Ls), or Thermus thermophilus (Tt). Sometimes the Cas13 is at least oneof LbuCas13a, LwaCas13a, LbaCas13a, HheCas13a, PprCas13a, EreCas13a,CamCas13a, or LshCas13a.

A workflow of a method for detecting a target nucleic acid in a samplewithin a fluidic device can include sample preparation, nucleic acidamplification, incubation with a programmable nuclease, and/or detection(readout). FIG. 9 shows a schematic illustrating a workflow of aprogrammable nuclease reaction. Step 1 shown in the workflow is samplepreparation, Step 2 shown in the workflow is nucleic acid amplification.Step 3 shown in the workflow is programmable nuclease incubation. Step 4shown in the workflow is detection (readout). Non-essential steps areshown as oval circles. Steps 1 and 2 are optional, and steps 3 and 4 canoccur concurrently, if incubation and detection of programmable nucleaseactivity are within the same chamber. Sample preparation andamplification can be carried out within a fluidic device describedherein or, alternatively, can be carried out prior to introduction intothe fluidic device. As mentioned above, sample preparation of anynucleic acid amplification are optional, and can be excluded. In furthercases, programmable nuclease reaction incubation and detection (readout)can be performed sequentially (one after another) or concurrently (atthe same time). In some embodiments, sample preparation and/oramplification can be performed within a first fluidic device and thenthe sample can be transferred to a second fluidic device to carry outSteps 3 and 4 and, optionally, Step 2.

Workflows and systems compatible with the compositions and methodsprovided herein include one-pot reactions and two-pot reactions. In aone-pot reaction, amplification, reverse transcription, amplificationand reverse transcription, or amplification and in vitro transcription,and detection can be carried out simultaneously in one chamber. In otherwords, in a one-pot reaction, any combination of reverse transcription,amplification, and in vitro transcription can be performed in the samereaction as detection. In a two-pot reaction, any combination of reversetranscription, amplification, and in vitro transcription can beperformed in a first reaction, followed by detection in a secondreaction. The one-pot or two-pot reactions can be carried out in any ofthe chambers of the devices disclosed herein.

A fluidic device for sample preparation can be referred to as afiltration device. In some embodiments, the filtration device for samplepreparation resembles a syringe or, comprises, similar functionalelements to a syringe. For example, a functional element of thefiltration device for sample preparation includes a narrow tip forcollection of liquid samples. Liquid samples can include blood, saliva,urine, or any other biological fluid. Liquid samples can also includeliquid tissue homogenates. The tip, for collection of liquid samples,can be manufactured from glass, metal, plastic, or other biocompatiblematerials. The tip may be replaced with a glass capillary that may serveas a metering apparatus for the amount of biological sample addeddownstream to the fluidic device. For some samples, e.g., blood, thecapillary may be the only fluidic device required for samplepreparation. Another functional element of the filtration device forsample preparation may include a channel that can carry volumes from nLto mL, containing lysis buffers compatible with the programmablenuclease reaction downstream of this process. The channel may bemanufactured from metal, plastic, or other biocompatible materials. Thechannel may be large enough to hold an entire fecal, buccal, nasal, orother biological sample collection swab. The filtration device mayfurther contain a solution of reagents that will lyse the cells in eachtype of samples and release the nucleic acids so that they areaccessible to the programmable nuclease. Active ingredients of thesolution may be chaotropic agents, detergents, salts, and can be of highosmolality, ionic strength and pH. Chaotropic agents or chaotropes aresubstances that disrupt the three-dimensional structure inmacromolecules such as proteins, DNA, or RNA. One example protocolcomprises a 4 M guanidinium isothiocyanate, 25 mM sodium citrate·2H₂0,0.5% (w/v) sodium lauryl sarcosinate, and 0.1 M β-mercaptoethanol), butnumerous commercial buffers for different cellular targets may also beused. Alkaline buffers may also be used for cells with hard shells,particularly for environmental samples. Detergents such as sodiumdodecyl sulphate (SDS) and cetyl trimethylammonium bromide (CTAB) mayalso be implemented to chemical lysis buffers. Cell lysis may also beperformed by physical, mechanical, thermal or enzymatic means, inaddition to chemically-induced cell lysis mentioned previously. Thedevice may include more complex architecture depending on the type ofsample, such as nanoscale barbs, nanowires, sonication capability in aseparate chamber of the device, integrated laser, integrated heater, forexample, a Peltier-type heater, or a thin-film planar heater, and/ormicrocapillary probes for electrical lysis. Any samples described hereincan be used in this workflow. For example samples may include liquidsamples collected from a subject being tested for a condition ofinterest. FIG. 10 shows an example fluidic, or filtration, device forsample preparation that may be used in Step 1 of the workflow schematicof FIG. 9 . The sample preparation fluidic device shown in this figurecan process different types of biological sample: finger-prick blood,urine or swabs with fecal, cheek or other collection.

A fluidic device may be used to carry out any one of, or any combinationof, Steps 2-4 of FIG. 9 (nucleic acid amplification, programmablenuclease reaction incubation, detection (readout)). FIG. 11 shows anexample fluidic device for a programmable nuclease reaction with afluorescence or electrochemical readout that may be used in Step 2 toStep 4 of the workflow schematic of FIG. 9 . This figure shows that thedevice performs three iterations of Steps 2 through 4 of the workflowschematic of FIG. 9 . At top, is one variation of this fluidic device,which performs the programmable nuclease reaction incubation anddetection (readout) steps, but not amplification. Shown in the middle isanother variation of said fluidic device, comprising a one-chamberreaction with amplification. Shown at bottom is yet another variation ofthe fluidic device, comprising a two-chamber reaction withamplification. An exploded view diagram summarizing the fluorescence andelectrochemical processes that may be used for detection of the reactionare shown in FIG. 12 .

In some embodiments, the fluidic device may be a pneumatic device. Thepneumatic device may comprise one or more sample chambers connected toone or more detection chambers by one or more pneumatic valves.Optionally, the pneumatic device may further comprise one or moreamplification chamber between the one or more sample chambers and theone or more detection chambers. The one or more amplification chambersmay be connected to the one or more sample chambers and the one or moredetection chambers by one or more pneumatic valves. A pneumatic valvemay be made from PDMS, or any other suitable material. A pneumatic valvemay comprise a channel perpendicular to a microfluidic channelconnecting the chambers and allowing fluid to pass between chambers whenthe valve is open. In some embodiments, the channel deflects downwardupon application of positive or negative air pressure and through thechannel perpendicular to the microfluidic channel.

In some embodiments, the fluidic device may be a sliding valve device.The sliding valve device may comprise a sliding layer with one or morechannels and a fixed layer with one or more sample chambers and one ormore detection chambers. Optionally, the fixed layer may furthercomprise one or more amplification chambers. In some embodiments, thesliding layer is the upper layer and the fixed layer is the lower layer.In other embodiments, the sliding layer is the lower layer and the fixedlayer is the upper layer. In some embodiments, the upper layer is madeof a plastic polymer comprising poly-methacrylate (PMMA), cyclic olefinpolymer (COP), cyclic olefin copolymer (COC), polyethylene (PE),high-density polyethylene (HDPE), polypropylene (PP); a glass; or asilicon. In some embodiments, the lower layer is made of a plasticpolymer comprising poly-methacrylate (PMMA), cyclic olefin polymer(COP), cyclic olefin copolymer (COC), polyethylene (PE), high-densitypolyethylene (HDPE), polypropylene (PP); a glass; or a silicon. Thesliding valve device may further comprise one or more of a side channelwith an opening aligned with an opening in the sample chamber, a sidechannel with an opening aligned with an opening in the amplificationchamber, or a side channel with an opening aligned with the opening inthe detection chamber. In some embodiments the side channels areconnected to a mixing chamber to allow transfer of fluid between thechambers. In some embodiments, the sliding valve device comprises apneumatic pump for mixing, aspirating, and dispensing fluid in thedevice.

The chip (also referred to as fluidic device) may be manufactured from avariety of different materials. Exemplary materials that may be usedinclude plastic polymers, such as poly-methacrylate (PMMA), cyclicolefin polymer (COP), cyclic olefin copolymer (COC), polyethylene (PE),high-density polyethylene (HDPE), polypropylene (PP); glass; andsilicon. Features of the chip may be manufactured by various processes.For example, features may be (1) embossed using injection molding, (2)micro-milled or micro-engraved using computer numerical control (CNC)micromachining, or non-contact laser drilling (by means of a CO2 lasersource); (3) additive manufacturing, and/or (4) photolithographicmethods.

The design may include up to three (3) input ports operated by three (3)pumps, labelled on FIG. 11 as P1-P3. The pumps may be operated byexternal syringe pumps using low pressure or high pressure. The pumpsmay be passive, and/or active (pneumatic, piezoelectric, Braille pin,electroosmotic, acoustic, gas permeation, or other).

The ports may be connected to pneumatic pressure pumps, air or gas maybe pumped into the microfluidic channels to control the injection offluids into the fluidic device. At least three reservoirs may beconnected to the device, each containing buffered solutions of: (1)sample, which may be a solution containing purified nucleic acidsprocessed in a separate fluidic device, or neat sample (blood, saliva,urine, stool, and/or sputum); (2) amplification mastermix, which variesdepending on the method used, wherein the method may include any ofloop-mediated isothermal amplification (LAMP), strand displacementamplification (SDA), recombinase polymerase amplification (RPA),helicase dependent amplification (HDA), multiple displacementamplification (MDA), rolling circle amplification (RCA), and nucleicacid sequence-based amplification (NASBA), transcription mediatedamplification (TMA), circular helicase dependent amplification (cHDA),exponential amplification reaction (EXPAR), ligase chain reaction (LCR),simple method amplifying RNA targets (SMART), single primer isothermalamplification (SPIA), hinge-initiated primer-dependent amplification ofnucleic acids (HIP), nicking enzyme amplification reaction (NEAR), orimproved multiple displacement amplification (IMDA); and (3)pre-complexed programmable nuclease mix, which includes one or moreprogrammable nuclease and guide oligonucleotides. The method of nucleicacid amplification may also be polymerase chain reaction (PCR), whichincludes cycling of the incubation temperature at different levels,hence is not defined as isothermal. Often, the reagents for nucleic acidamplification comprise a recombinase, a oligonucleotide primer, asingle-stranded DNA binding (SSB) protein, and a polymerase. Sometimes,nucleic acid amplification of the sample improves at least one ofsensitivity, specificity, or accuracy of the assay in detecting thetarget nucleic acid. In some cases, the nucleic acid amplification isperformed in a nucleic acid amplification region on the support medium.Alternatively or in combination, the nucleic acid amplification isperformed in a reagent chamber, and the resulting sample is applied tothe support medium. Sometimes, the nucleic acid amplification isisothermal nucleic acid amplification. Complex formation of a nucleasewith guides (a programmable nuclease) and reporter probes may occur offthe chip. An additional port for output of the final reaction productsis depicted at the end of the fluidic path, and is operated by a similarpump, as the ones described for P1-P3. The reactions product can be,thus, collected for additional processing and/or characterization, e.g.,sequencing.

The flow of liquid in this fluidic device may be controlled using up tofour (4) microvalves, labelled in FIG. 11 as V1-V4. These valves can beelectro-kinetic microvalves, pneumatic microvalves, vacuum microvalves,capillary microvalves, pinch microvalves, phase-change microvalves,burst microvalves.

The flow to and from the fluidic channel from each of P1-P4 iscontrolled by valves, labelled as V1-V4. The volume of liquids pumpedinto the ports can vary from nL to mL depending in the overall size ofthe device.

In device iteration 2.1, shows in FIG. 11 , no amplification is needed.After addition of sample and pre-complexed programmable nuclease mix inP1 and P2, respectively, the reagents may be mixed in the serpentinechannel, S1, which then leads to chamber C1 where the mixture may beincubated at the required temperature and time. The readout can be donesimultaneously in C1, described in FIG. 12 . Thermoregulation in C1 maybe carried out using a thin-film planar heater manufactured, from e.g.Kapton, or other similar materials, and controlled by a proportionalintegral derivative (PID).

In device iteration 2.2, shown in FIG. 11 , after addition of sample,amplification mix, and pre-complexed programmable nuclease mix in P1, P2and P3, respectively, the reagents can be mixed in the serpentinechannel, S1, which then leads to chamber C1 where the mixture isincubated at the required temperature and time needed to efficientamplification, as per the conditions of the method used. The readout maybe done simultaneously in C1, described in FIG. 12 . Thermoregulationmay be achieved as previously described.

In device iteration 2.3, shown in FIG. 11 , amplification andprogrammable nuclease reactions occur in separate chambers. Thepre-complexed programmable nuclease mix is pumped into the amplifiedmixture from C1 using pump P3. The liquid flow is controlled by valveV3, and directed into serpentine mixer S2, and subsequently in chamberC2 for incubation the required temperature, for example at 37° C. for 90minutes.

During the detection step (shown as step 4 in the workflow diagram ofFIG. 9 ), the Cas-gRNA complex binds to its matching nucleic acid targetfrom the amplified sample and is activated into a non-specific nuclease,which cleaves a nucleic acid-based reporter molecule to generate asignal readout. In the absence of a matching nucleic acid target, theCas-gRNA complex does not cleave the nucleic acid-based reportermolecule. Real-time detection of the Cas reaction can be achieved bythree methods: (1) fluorescence, (2) electrochemical detection, and (3)electrochemiluminescence. All three methods are described below and aschematic diagrams of these processes is shown in FIG. 12 . Detection ofthe signal can be achieved by multiple methods, which can detect asignal that is calorimetric, potentiometric, amperometric, optical(e.g., fluorescent, colorometric, etc.), or piezo-electric, asnon-limiting examples.

FIG. 12 shows schematic diagrams of a readout process that may be usedin conjunction with a fluidic device (e.g., the fluidic device of FIG.11 ), including (a) fluorescence readout and (b) electrochemicalreadout. The emitted fluorescence of cleaved reporter oligo nucleotidesmay be monitored using a fluorimeter positioned directly above thedetection and incubation chamber. The fluorimeter may be a commerciallyavailable instrument, the optical sensor of a mobile phone or smartphone, or a custom-made optical array comprising of fluorescenceexcitation means, e.g. CO2, other, laser and/or light emitting diodes(LEDs), and fluorescence detection means e.g. photodiode array,phototransistor, or others.

The fluorescence detection and excitation may be multiplexed, wherein,for example, fluorescence detection involves exciting and detecting morethan one fluorophore in the incubation and detection chamber (C1 or C2).The fluorimeter itself may be multichannel, in which detecting andexciting light at different wavelengths, or more than one fluorimetermay be used in tandem, and their position above the incubation anddetection chamber (C1 and C2) be modified by mechanical means, such as amotorized mechanism using micro or macro controllers and actuators(electric, electronic, and/or piezo-electric).

Two electrochemical detection variations are described herein, usingintegrated working, counter and reference electrodes in the incubationand detection chamber (C1 or C2):

Increase in signal. The progress of the cleavage reaction catalyzed bythe programmable nuclease may be detected using a streptavidin-biotincoupled reaction. The top surface of the detection and incubationchamber may be functionalized with nucleic acid molecules (ssRNA, ssDNAor ssRNA/DNA hybrid molecules) conjugated with a biotin moiety. Thebottom surface of the detection and incubation chamber operates as anelectrode, comprising of working, reference, and counter areas,manufactured (or screen-printed) from carbon, graphene, silver, gold,platinum, boron-doped diamond, copper, bismuth, titanium, antimony,chromium, nickel, tin, aluminum, molybdenum, lead, tantalum, tungsten,steel, carbon steel, cobalt, indium tin oxide (ITO), ruthenium oxide,palladium, silver-coated copper, carbon nano-tubes, or other metals. Thebottom surface of the detection and incubation chamber may be coatedwith streptavidin molecules. In the absence of any biotin molecules, thecurrent measured by a connected electrochemical analyzer (commercial, orcustom-made) is low. When the pre-complexed programmable nuclease mixwith amplified target flows in the detection and incubation chamber, andis activated at a higher temperature, for example at 37° C., cleavage ofthe single-stranded nucleic acid (ssNA) linker releases biotin moleculesthat can diffuse onto the streptavidin-coated bottom surface of thedetection and incubation chamber. Because of the interaction of biotinand streptavidin molecules, an increase in the current is read by acoupled electrochemical analyzer.

Other types of signal amplification that use enrichment may also be usedapart from biotin-streptavidin excitation. Non-limiting examples are:(1) glutathione, glutathione S-transferase, (2) maltose, maltose-bindingprotein, (3) chitin, chitin-binding protein.

Decrease in signal. The progress of the programmable nuclease cleavagereaction may be monitored by recording the decrease in the currentproduced by a ferrocene (Fc), or other electroactive mediator moieties,conjugated to the individual nucleotides of nucleic acid molecules(ssRNA, ssDNA or ssRNA/DNA hybrid molecules) immobilized on the bottomsurface of the detection and incubation chamber. In the absence of theamplified target, the programmable nuclease complex remains inactive,and a high current caused by the electroactive moieties is recorded.When the programmable nuclease complex with guides flows in thedetection and incubation chamber and is activated by the matchingnucleic acid target at 37° C., the programmable nuclease complexnon-specifically degrades the immobilized Fc-conjugated nucleic acidmolecules. This cleavage reaction decreases the number of electroactivemolecules and, thus, leads to a decrease in recorded current.

The electrochemical detection may also be multiplexed. This is achievedby the addition of one or more working electrodes in the incubation anddetection chamber (C1 or C2). The electrodes can be plain, or modified,as described above for the single electrochemical detection method.

Electrochemiluminescence in a combined optical and electrochemicalreadout method. The optical signal may be produced by luminescence of acompound, such as tri-propyl amine (TPA) generated as an oxidationproduct of an electroactive product, such as ruthenium bipyridine,[Ru(py)3]2+.

A number of different programmable nuclease proteins may be multiplexedby: (1) separate fluidic paths (parallelization of channels), mixed withthe same sample, for each of the proteins, or (2) switching to digital(two-phase) microfluidics, where each individual droplet contains aseparate reaction mix. The droplets could be generated from single ordouble emulsions of water and oil. The emulsions are compatible withprogrammable nuclease reaction, and optically inert.

FIG. 13 shows an example fluidic device for coupled invertase/Casreactions with colorimetric or electrochemical/glucometer readout. Thisdiagram illustrates a fluidic device for miniaturizing a Cas reactioncoupled with the enzyme invertase. Surface modification and readoutprocesses are depicted in exploded view schemes at the bottom including(a) optical readout using DNS, or other compound and (b) electrochemicalreadout (electrochemical analyzer or glucometer). Described herein isthe coupling of the Cas reaction with the enzyme invertase (EC3.2.1.26), or sucrase or β-fructofuranosidase. This enzyme catalyzes thebreakdown of sucrose to fructose and glucose.

The following methods may be used to couple the readout of the Casreaction to invertase activity:

Colorimetry using a camera, standalone, or an integrated mobile phoneoptical sensor. The amount of fructose and glucose is linked to acolorimetric reaction. Two examples are: (a) 3,5-Dinitrosalicylic acid(DNS), and (b) formazan dye thiazolyl blue. The color change can bemonitored using a CCD camera, or the image sensor of a mobile phone. Forthis method, we use a variation of the fluidic device described in FIG.13 . The modification is the use of a camera, instead of a fluorimeterabove C3.

Amperometry using a conventional glucometer, or an electrochemicalanalyzer. A variation of the fluidic device described in FIG. 11 may beused, for example, the addition of one more incubation chamber C3. Anadditional step is added to the reaction scheme, which takes place inchamber C2. The top of the chamber surface is coated with singlestranded nucleic acid that is conjugated to the enzyme invertase (Inv).The target-activated programmable nuclease complex cleaves the invertaseenzyme from the oligo (ssRNA, ssDNA or ssRNA/DNA hybrid molecule), inC2, and invertase is then available to catalyze the hydrolysis ofsucrose injected by pump P4, and controlled by valve V4. The mixture ismixed in serpentine mixer S3, and at chamber C3, the glucose producedmay be detected colorimetrically, as previously described,electrochemically. The enzyme glucose oxidase is dried on the surface onC3, and catalyzes the oxidation of glucose to hydrogen peroxide andD-glucono-δ-lactone.

A number of different devices are compatible with detection of targetnucleic acids using the methods and compositions disclosed herein. Insome embodiments, the device is any of the microfluidic devicesdisclosed herein. In other embodiments, the device is a lateral flowtest strip connected to a reaction chamber. In further embodiments, thelateral flow strip may be connected to a sample preparation device.

In some embodiments, the fluidic device may be a pneumatic device. Thepneumatic device may comprise one or more sample chambers connected toone or more detection chambers by one or more pneumatic valves.Optionally, the pneumatic device may further comprise one or moreamplification chamber between the one or more sample chambers and theone or more detection chambers. The one or more amplification chambersmay be connected to the one or more sample chambers and the one or moredetection chambers by one or more pneumatic valves. A pneumatic valvemay be made from PDMS, or any other suitable material. A pneumatic valvemay comprise a channel perpendicular to a microfluidic channelconnecting the chambers and allowing fluid to pass between chambers whenthe valve is open. In some embodiments, the channel deflects downwardupon application of positive or negative air pressure and through thechannel perpendicular to the microfluidic channel.

In some embodiments, the fluidic device may be a sliding valve device.The sliding valve device may comprise a sliding layer with one or morechannels and a fixed layer with one or more sample chambers and one ormore detection chambers. Optionally, the fixed layer may furthercomprise one or more amplification chambers. In some embodiments, thesliding layer is the upper layer and the fixed layer is the lower layer.In other embodiments, the sliding layer is the lower layer and the fixedlayer is the upper layer. In some embodiments, the upper layer is madeof a plastic polymer comprising poly-methacrylate (PMMA), cyclic olefinpolymer (COP), cyclic olefin copolymer (COC), polyethylene (PE),high-density polyethylene (HDPE), polypropylene (PP); a glass; or asilicon. In some embodiments, the lower layer is made of a plasticpolymer comprising poly-methacrylate (PMMA), cyclic olefin polymer(COP), cyclic olefin copolymer (COC), polyethylene (PE), high-densitypolyethylene (HDPE), polypropylene (PP); a glass; or a silicon. Thesliding valve device may further comprise one or more of a side channelwith an opening aligned with an opening in the sample chamber, a sidechannel with an opening aligned with an opening in the amplificationchamber, or a side channel with an opening aligned with the opening inthe detection chamber. In some embodiments the side channels areconnected to a mixing chamber to allow transfer of fluid between thechambers. In some embodiments, the sliding valve device comprises apneumatic pump for mixing, aspirating, and dispensing fluid in thedevice.

Pneumatic Valve Device. A microfluidic device particularly well suitedfor carrying out the DETECTR reactions described herein is onecomprising a pneumatic valve, also referred to as a “quake valve”. Thepneumatic valve can be closed and opened by the flow of air from, for anexample, an air manifold. The opening of the pneumatic valve can lead toa downward deflection of the channel comprising the pneumatic valve,which can subsequently deflect down towards and seal off a microfluidicchannel beneath the channel comprising the pneumatic valve. This canlead to stoppage of fluid flow in the microfluidic channel. When the airmanifold is turned off, the flow of air through the channel comprisingthe quake valve ceases and the microfluidic channel beneath the channelcomprising the quake valve is “open”, and fluid can flow through. Insome embodiments, the channel comprising the pneumatic valve may beabove or below the microfluidic channel carrying the fluid of interest.In some embodiments, the channel comprising the pneumatic valve can beparallel or perpendicular to the microfluidic channel carrying the fluidof interest. Pneumatic valves can be made of a two hard thermoplasticlayers sandwiching a soft silicone layer.

One example layout that is compatible with the compositions and methodsdisclosed herein is shown in FIG. 100 and FIG. 100 . In someembodiments, the device comprises a sample chamber and a detectionchamber, wherein the detection chamber is fluidically connected to thesample chamber by a pneumatic valve and wherein the detection chambercomprises any programmable nuclease of the present disclosure.Optionally, the device can also include an amplification chamber that isbetween the fluidic path from the sample chamber to the detectionchamber, is connected to the sample chamber by a pneumatic valve, and isadditionally connected to the detection chamber by a pneumatic valve. Insome embodiments, the pneumatic valve is made of PDMS, or any othermaterial for forming microfluidic valves. In some embodiments, thesample chamber has a port for inserting a sample. The sample can beinserted using a swab. The sample chamber can have a buffer for lysingthe sample. The sample chamber can have a filter between the chamber andthe fluidic channel to the amplification or detection chambers. Thesample chamber may have an opening for insertion of a sample. A samplecan be incubated in the sample chamber for from 30 seconds to 10minutes. The air manifold may until this point be on, pushing airthrough the pneumatic valve and keeping the fluidic channel between thesample chamber and the amplification or detection chambers closed. Atthis stage, the air manifold can be turned off, such that no air ispassing through the pneumatic valve, and allowing the microfluidicchannel to open up and allow for fluid flow from the sample chamber tothe next chamber (e.g., the amplification or detection chambers). Indevices where there is an amplification chamber, the lysed sample flowsfrom the sample chamber into the amplification chamber. Otherwise, thelysed sample flows from the sample chamber into the detection chamber.At this stage, the air manifold is turned back on, to push air throughthe pneumatic valve and seal the microfluidic channel. The amplificationchamber holds various reagents for amplification and, optionally,reverse transcription of a target nucleic acid in the sample. Thesereagents may include forward and reverse primers, a deoxynucleotidetriphosphate, a reverse transcriptase, a T7 promoter, a T7 polymerase,or any combination thereof. The sample is allowed to incubate in theamplification chamber for from 5 minutes to 40 minutes. The amplifiedand, optionally reverse transcribed, sample is moved into the detectionchamber as described above: the air manifold is turned off, ceasing airflow through the pneumatic valve and opening the microfluidic channel.The detection chamber can include any programmable nuclease disclosedherein, a guide RNA with a portion reverse complementary to a portion ofthe target nucleic acid, and any reporter disclosed herein. In someembodiments, the detection chamber may comprise a plurality of guideRNAs. The plurality of guide RNAs may have the same sequence, or one ormore of the plurality of guide RNAs may have different sequences. Insome embodiments, the plurality of guide RNAs has a portion reversecomplementary to a portion of a target nucleic acid different than asecond RNA of the plurality of guide RNAs. The plurality of guide RNAsmay comprise at least 5, at least 10, at least 15, at least 20, or atleast 50 guide RNAs. Once the sample is moved into the detectionchamber, the DETECTR reaction can be carried out for 1 minute to 20minutes. Upon hybridization of the guide RNA to the target nucleic acid,the programmable nuclease is activated and begins to collaterally cleavethe reporter, which as described elsewhere in this disclosure has anucleic acid and one or more molecules that enable detection ofcleavage. The detection chamber can interface with a device for readingout for the signal. For example, in the case of a colorimetric orfluorescence signal generated upon cleavage, the detection chamber maybe coupled to a spetrophotometer or fluorescence reader. In the casewhere an electrochemical signal is generated, the detection chamber mayhave one to 10 metal leads connected to a readout device (e.g., aglucometer), as shown in FIG. 107 . FIG. 106 shows a schematic of thetop layer of a cartridge of a pneumatic valve device of the presentdisclosure, highlighting suitable dimensions. The schematic shows onecartridge that is 2 inches by 1.5 inches. FIG. 107 shows a schematic ofa modified top layer of a cartridge of a pneumatic valve device of thepresent disclosure adapted for electrochemical dimension. In thisschematic, three lines are shown in the detection chambers (4 chambersat the very right). These three lines represent wiring (or “metalleads”), which is co-molded, 3D-printed, or manually assembled in thedisposable cartridge to form a three-electrode system. Electrodes aretermed as working, counter, and reference. Electrodes can also bescreenprinted on the cartridges. Metals used can be carbon, gold,platinum, or silver. A major advantage of the pneumatic valve device isthat the pneumatic valves connecting the various chambers of the deviceprevent backflow from chamber to chamber, which reduces contamination.Prevention of backflow and preventing sample contamination is especiallyimportant for the applications described herein. Sample contaminationcan result in false positives or can generally confound the limit ofdetection for a target nucleic acid. As another example, the pneumaticvalves disclosed herein are particularly advantageous for devices andmethods for multiplex detection. In multiplexed assays, where two ormore target nucleic acids are assayed for, it is particularly importantthat backflow and contamination is avoided. Backflow between chambers ina multiplexed assay can lead to cross-contamination of different guidenucleic acids or different programmably nuclease and can result in falseresults. Thus, the pneumatic valve device, which is designed to minimizeor entirely avoid backflow, is particularly superior, in comparison toother device layouts, for carrying out the detection methods disclosedherein.

FIG. 100 shows a pneumatic valve device layout for a DETECTR assay. FIG.100A shows a schematic of a pneumatic valve device. A pipette pumpaspirates and dispenses samples. An air manifold is connected to apneumatic pump to open and close the normally closed valve. Thepneumatic device moves fluid from one position to the next. Thepneumatic valve device design has reduced channel cross talk compared toother device designs. FIG. 100B shows a schematic of a cartridge for usein the pneumatic valve device shown in FIG. 100A. The valveconfiguration is shown. The normally closed valves (one such valve isindicated by an arrow) comprise an elastomeric seal on top of thechannel to isolate each chamber from the rest of the system when thechamber is not in use. The pneumatic pump uses air to open and close thevalve as needed to move fluid to the necessary chambers within thecartridge. FIG. 101 shows a valve circuitry layout for the pneumaticvalve device shown in FIG. 100A. A sample is placed in the sample wellwhile all valves are closed, as shown at (i.). The sample is lysed inthe sample well. The lysed sample is moved from the sample chamber to asecond chamber by opening the first quake valve, as shown at (ii.), andaspirating the sample using the pipette pump. The sample is then movedto the first amplification chamber by closing the first quake valve andopening a second quake valve, as shown at (iii.) where it is mixed withthe amplification mixture. After the sample is mixed with theamplification mixture, it is moved to a subsequent chamber by closingthe second quake valve and opening a third quake valve, as shown at(iv). The sample is moved to the DETECTR chamber by closing the thirdquake valve and opening a fourth quake valve, as shown at (v). Thesample can be moved through a different series of chambers by openingand closing a different series of quake valves, as shown at (vi).Actuation of individual valves in the desired chamber series preventscross contamination between channels. In some embodiments the slidingvalve device has a surface area of 5 cm by 5 cm, 5 by 6 cm, 6 by 7 cm, 7by 8 cm, 8 by 9 cm, 9 by 10 cm, 10 by 11 cm, 11 by 12 cm, 6 by 9 cm, 7by 10 cm, 8 by 11 cm, 9 by 12 cm, 10 by 13 cm, 11 by 14 cm, 12 by 11 cm,about 30 sq cm, about 35 sq cm, about 40 sq cm, about 45 sq cm, about 50sq cm, about 55 sq cm, about 60 sq cm, about 65 sq cm, about 70 sq cm,about 75 sq cm, about 25 sq cm, about 20 sq cm, about 15 sq cm, about 10sq cm, about 5 sq cm, from 1 to 100 sq cm, from 5 to 10 sq cm, from 10to 15 sq cm, from 15 to 20 sq cm, from 20 to 25 sq cm, from 25 to 30 sqcm, from 30 to 35 sq cm, from 35 to 40 sq cm, from 40 to 45 sq cm, from45 to 50 sq cm, from 5 to 90 sq cm, from 10 to 0 sq cm, from 15 to 5 sqcm, from 20 to 10 sq cm, or from 25 to 15 sq cm.

In one embodiment, a pneumatic valve device has the following layout.The device has a first chamber for sample lysis, a second chamber fordetection, and a third chamber for amplification. Another way ofreferring to these chambers is a sample chamber (e.g., the firstchamber), a detection chamber (e.g., the second chamber), and anamplification chamber (e.g., the third chamber). In this layout, thepresent disclosure provides a device for measuring a signal comprising:i) a first chamber comprising a sample and a buffer for lysing thesample; and ii) a second chamber, fluidically connected by a firstpneumatic valve to the first chamber, wherein the second chambercomprises a programmable nuclease and a reporter comprising a nucleicacid and a detection moiety, and wherein the second chamber is coupledto a measurement device for measuring the signal from the detectionmoiety produced by cleavage of the nucleic acid of the reporter. Thedevice further comprises iii) a third chamber fluidically connected bythe first pneumatic valve to the first chamber and connected by a secondpneumatic valve to the second chamber. In this embodiment, the firstpneumatic valve fluidically connecting the first chamber and the secondchamber comprises a first channel adjacent to a first microfluidicchannel connecting the first chamber and the second chamber.Additionally, the first pneumatic valve fluidically connecting the firstchamber and the third chamber comprises a second channel adjacent to asecond microfluidic channel connecting the first chamber and the thirdchamber. The second pneumatic valve fluidically connecting the secondchamber and the third chamber comprises a third channel adjacent to athird microfluidic channel connecting the second chamber and the thirdchamber. Further, the first channel, the second channel, or the thirdchannels are connected to an air manifold. In this embodiment, thesecond chamber additionally includes a guide nucleic acid. In a variantof this pneumatic device, more than one chamber comprising aprogrammable nuclease and a reporter are fluidically connected to asingle chamber comprising the sample. Further, more than one chambercomprises a programmable nuclease and a reporter are fluidicallyconnected to a single chamber comprising the forward primer, the reverseprimer, the dNTP, and the polymerase.

In another embodiment, a pneumatic device has the following layout. Thedevice has a first chamber for sample lysis and a second chamber fordetection. Another way of referring to these chambers is a samplechamber (e.g., the first chamber) and a detection chamber (e.g., thesecond chamber). In this layout, the present disclosure provides adevice for measuring a signal comprising: i) a first chamber comprisinga sample and a buffer for lysing the sample; and ii) a second chamber,fluidically connected by a first pneumatic valve to the first chamber,wherein the second chamber comprises a programmable nuclease and areporter comprising a nucleic acid and a detection moiety, and whereinthe second chamber is coupled to a measurement device for measuring thesignal from the detection moiety produced by cleavage of the nucleicacid of the reporter. In this embodiment, the first pneumatic valvefluidically connecting the first chamber and the second chambercomprises a first channel adjacent to a first microfluidic channelconnecting the first chamber and the second chamber. Further, the firstchannel is connected to an air manifold. In this embodiment, the secondchamber additionally includes a guide nucleic acid. In a variant of thispneumatic device, more than one chamber comprising a programmablenuclease and a reporter are fluidically connected to a single chambercomprising the sample.

Sliding Valve Device. A microfluidic device particularly well suited forcarrying out the DETECTR reactions described herein is a sliding valvedevice. The sliding valve device can have a sliding layer and a fixedlayer. The sliding layer may be on top and the fixed layer may be onbottom. Alternatively, the sliding layer may be on bottom and the fixedlayer may be on top. In some embodiments, the sliding valve has achannel. The channel can have an opening at one end that interacts withan opening in a chamber and the channel can also have an opening at theother end that interacts with an opening in a side channel. In someembodiments, the sliding layer has more than one opening. In someembodiments, the fixed layer comprises a sample chamber, anamplification chamber, and a detection chamber. The sample chamber, theamplification chamber, and the detection layer can all have an openingat the bottom of the chambers. For example, the sample chamber may havean opening for insertion of a sample. When the opening in a chamber isaligned with the opening in a channel, fluid can flow from the chamberinto the channel. Further, when the opening in the channel issubsequently aligned with an opening in a side channel, fluid can flowfrom the channel into the side channel. The side channel can be furtherfluidically connected to a mixing chamber, or a port in which aninstrument (e.g., a pipette pump) for mixing fluid is inserted.Alignment of openings can be enabled by physically moving orautomatically actuating the sliding layer to slide along the length ofthe fixed layer. In some embodiment, the above described pneumaticvalves can be added at any position to the sliding valve device in orderto control the flow of fluid from one chamber into the next. The slidingvalve device can also have multiple layers. For example, the slidingvalve can have 2, 3, 4, 5, 6, 7, 8, 9, 10, or more layers.

FIG. 90 shows a layout for a DETECTR assay. Shown at top is a pneumaticpump, which interfaces with the cartridge. Shown at middle is a top downview of the cartridge showing a top layer with reservoirs. Shown atbottom is a sliding valve containing the sample and arrows pointing tothe lysis chamber at left, following by amplification chambers to theright, and DETECT chambers further to the right. FIG. 102 shows aschematic of a sliding valve device. The offset pitch of the channelsallows aspirating and dispensing into each well separately and helps tomitigate cross talk between the amplification chambers and correspondingchambers. FIG. 103 shows a diagram of sample movement through thesliding valve device shown in FIG. 102 . In the initial closed position(i.), the sample is loaded into the sample well and lysed. The slidingvalve is then actuated by the instrument, and samples are loaded intoeach of the channels using the pippette pump, which dispenses theappropriate volume into the channel (ii.). The sample is delivered tothe amplification chambers by actuating the sliding valve and mixed withthe pipette pump (iii.). Samples from the amplification chamber areaspirated into each channel (iv.) and then dispensed and mixed into eachDETECTR chamber (v.) by actuating the sliding valve and pipette pump. Insome embodiments the sliding valve device has a surface area of 5 cm by8 cm, 5 by 6 cm, 6 by 7 cm, 7 by 8 cm, 8 by 9 cm, 9 by 10 cm, 10 by 11cm, 11 by 12 cm, 6 by 9 cm, 7 by 10 cm, 8 by 11 cm, 9 by 12 cm, 10 by 13cm, 11 by 14 cm, 12 by 11 cm, about 30 sq cm, about 35 sq cm, about 40sq cm, about 45 sq cm, about 50 sq cm, about 55 sq cm, about 60 sq cm,about 65 sq cm, about 70 sq cm, about 75 sq cm, about 25 sq cm, about 20sq cm, about 15 sq cm, about 10 sq cm, about 5 sq cm, from 1 to 100 sqcm, from 5 to 10 sq cm, from 10 to 15 sq cm, from 15 to 20 sq cm, from20 to 25 sq cm, from 25 to 30 sq cm, from 30 to 35 sq cm, from 35 to 40sq cm, from 40 to 45 sq cm, from 45 to 50 sq cm, from 5 to 90 sq cm,from 10 to 0 sq cm, from 15 to 5 sq cm, from 20 to 10 sq cm, or from 25to 15 sq cm.

In one embodiment, a sliding valve device has the following layout. Thedevice has a first chamber for sample lysis, a second chamber fordetection, and a third chamber for amplification. Another way ofreferring to these chambers is a sample chamber (e.g., the firstchamber), a detection chamber (e.g., the second chamber), and anamplification chamber (e.g., the third chamber). In this layout, thepresent disclosure provides a device for measuring a signal comprises: asliding layer comprising a channel with an opening at a first end of thechannel and an opening at a second end of the channel; and a fixed layercomprising: i) a first chamber having an opening; ii) a second chamberhaving an opening, wherein the second chamber comprises a programmablenuclease and a reporter comprising a nucleic acid and a detectionmoiety; iii) a first side channel having an opening aligned with theopening of the first chamber; and iv) a second side channel having anopening aligned with the opening of the second chamber, wherein thesliding layer and the fixed layer move relative to each other tofluidically connect the first chamber and the first side channel via theopening at the first end of the channel, the opening at the second endof the channel, the opening of the first chamber, and the opening of thefirst side channel, and wherein the sliding layer and the fixed layermove relative to each other to fluidically connect the second chamberand the second side channel via the opening at the first end of thechannel, the opening at the second end of the channel, the opening ofthe second chamber, and the opening of the second side channel. Thefixed layer further comprises i) a third chamber having an opening; andii) a third side channel having an opening aligned with the opening ofthe third chamber, wherein the sliding layer and the fixed layer moverelative to each other to fluidically connect the third chamber and thethird side channel via the opening at the first end of the channel, theopening at the second end of the channel, the opening of the thirdchamber, and the opening of the third side channel. The second chamberis coupled to a measurement device for measuring the signal from thedetection moiety produced by cleavage of the nucleic acid of thereporter. Additionally, the opening of the first end of the channeloverlaps with the opening of the first chamber and the opening of thesecond end of the channel overlaps with the opening of the first sidechannel. The opening of the first end of the channel overlaps with theopening of the second chamber and the opening of the second end of thechannel overlaps with the opening of the second side channel. Theopening of the first end of the channel overlaps with the opening of thethird chamber and the opening of the second end of the channel overlapswith the opening of the third channel. Additionally, the first sidechannel, the second side channel, and the third side channel arefluidically connected to a mixing chamber. In this embodiment, thesecond chamber additionally includes a guide nucleic acid.

In another embodiment, a sliding valve device has the following layout.The device has a first chamber for sample lysis and a second chamber fordetection. Another way of referring to these chambers is a samplechamber (e.g., the first chamber) and a detection chamber. In thislayout, the present disclosure provides a device for measuring a signalcomprises: a sliding layer comprising a channel with an opening at afirst end of the channel and an opening at a second end of the channel;and a fixed layer comprising: i) a first chamber having an opening; ii)a second chamber having an opening, wherein the second chamber comprisesa programmable nuclease and a reporter comprising a nucleic acid and adetection moiety; iii) a first side channel having an opening alignedwith the opening of the first chamber; and iv) a second side channelhaving an opening aligned with the opening of the second chamber,wherein the sliding layer and the fixed layer move relative to eachother to fluidically connect the first chamber and the first sidechannel via the opening at the first end of the channel, the opening atthe second end of the channel, the opening of the first chamber, and theopening of the first side channel, and wherein the sliding layer and thefixed layer move relative to each other to fluidically connect thesecond chamber and the second side channel via the opening at the firstend of the channel, the opening at the second end of the channel, theopening of the second chamber, and the opening of the second sidechannel. The second chamber is coupled to a measurement device formeasuring the signal from the detection moiety produced by cleavage ofthe nucleic acid of the reporter. Additionally, the opening of the firstend of the channel overlaps with the opening of the first chamber andthe opening of the second end of the channel overlaps with the openingof the first side channel. The opening of the first end of the channeloverlaps with the opening of the second chamber and the opening of thesecond end of the channel overlaps with the opening of the second sidechannel. Additionally, the first side channel and the second sidechannel are fluidically connected to a mixing chamber. In thisembodiment, the second chamber additionally includes a guide nucleicacid.

Lateral Flow Devices. In some embodiments, a device of the presentdisclosure comprises a chamber and a lateral flow strip. FIG. 73 -FIG.74 shows a particularly advantageous layout for the lateral flow stripand a corresponding suitable reporter. FIG. 73 shows a modified Casreporter comprising a DNA linker to biotin-dT (shown as a pink hexagon)bound to a FAM molecule (shown as a green start). FIG. 74 shows thelayout of Milenia HybridDetect strips with the modified Cas reporter.This particular layout improvest the test result by generating highersignal in the case of a positive result, while also minimizing falsepositives. In this assay layout, the reporter comprises a biotin and afluorophore attached at one of a nucleic acid. The nucleic acid can bedirectly conjugated to the biotin molecule and the biotin can bedirectly conjugated to the fluorophore or the nucleic acid can bedirectly conjugated to the fluorophore and the fluorophore can bedirectly conjugated to the biotin. In this context, “directlyconjugated” indicated that no intervening molecules, polypeptides,proteins, or other moieties are present between the two moietiesdirectly conjugated to each other. For example, if a reporter comprisesa nucleic acid directly conjugated to a biotin and a biotin directlyconjugated to a fluorophore—no intervening moiety is present between thenucleic acid and the biotin and no intervening moiety is present betweenthe biotin and the fluorophore. Other affinity molecules, includingthose described herein can be used instead of biotin. Any of thefluorophores disclosed herein can also be used in the reporter. Thereporter can be suspended in solution or immobilized on the surface ofthe Cas chamber. Alternatively, the reporter can be immobilized onbeads, such as magnetic beads, in the reaction chamber where they areheld in position by a magnet placed below the chamber. When the reporteris cleaved by an activated programmable nuclease, the cleavedbiotin-fluorophore accumulates at the first line, which comprises astreptavidin (or another capture molecule such asglutathione-S-transferase, maltose-binding protein, chitin-bindingprotein). Gold nanoparticles, which are on the sample pad and flown ontothe strip using a chase buffer, are coated with an anti-fluorophoreantibody allowing binding and accumulation of the gold nanoparticle atthe first line. The nanoparticles additionally accumulate at a secondline which is coated with an antibody (e.g., anti-rabbit) against theantibody coated on the gold nanoparticles (e.g., rabbit, anti-FAM). Inthe case of a negative result, the reporter is not cleaved and does notflow on the lateral flow strip. Thus, the nanoparticles only bind andaccumulate at the second line Multiplexing on the lateral flow strip canbe performed by having two reporters (e.g., a biotin-FAM reporter and abiotin-DIG reporter). Anti-FAM and anti-DIG antibodies are coated ontothe lateral flow strip at two different regions. Anti-biotin antibodiesare coated on gold nanoparticles. Fluorophores are conjugated directlyto the affinity molecules (e.g., biotin) by first generating abiotin-dNTP following from the nucleic acids of the reporter and thenconjugating the fluorophore. In some embodiments, the lateral flow stripcomprises multiple layers.

In some embodiments, the above lateral flow strip can be additionallyinterfaced with a sample preparation device, as shown in FIG. 28 andFIG. 29 . FIG. 28 shows individual parts of sample preparation devicesof the present disclosure. Part A of the figure shows a single chambersample extraction device: (a) the insert holds the sample collectiondevice and regulates the step between sample extraction and dispensingthe sample into another reaction or detection device, (b) the singlechamber contains extraction buffer. Part B of the figure shows fillingthe dispensing chamber with material that further purifies the nucleicacid as it is dispensed is an option: (a) the insert holds the samplecollection device and regulates the “stages” of sample extraction andnucleic acid amplification. Each set of notches (red, blue and green)are offset 900 from the preceding set, (b) the reaction module containsmultiple chambers separated by substrates that allow for independentreactions to occur. (e.g., i. a nucleic acid separation chamber, ii. anucleic acid amplification chamber and iii. a DETECTR reaction chamberor dispensing chamber). Each chamber has notches (black) that preventthe insert from progressing into the next chamber without a deliberate900 turn. The first two chambers may be separated by material thatremoves inhibitors between the extraction and amplification reactions.Part C shows options for the reaction/dispensing chamber: (a) a singledispensing chamber may release only extracted sample orextraction/amplification extraction/amplification/DETECTR reactions, (b)a duel dispensing chamber may release extraction/multiplex amplificationproducts, and (c) a quadruple dispensing chamber would allow formultiplexing amplification and single DETECTR or four singleamplification reactions. FIG. 29 shows a sample work flow using a sampleprocessing device. The sample collection device is attached to theinsert portion of the sample processing device (A). The insert is placedinto the device chamber and pressed until the first stop (lower tabs ontop portion meet upper tabs on bottom portion) (B). This step allows thesample to come into contact with the nucleic acid extraction reagents.After the appropriate amount of time, the insert is turned 900 (C) anddepressed (D) to the next set of notches. These actions transfer thesample into the amplification chamber. The sample collection device isno longer in contact with the sample or amplification products. Afterthe appropriate incubation, the insert is rotated 900 (E) and depressed(F) to the next set of notches. These actions release the sample intothe DETECTR (green reaction). The insert is again turned 900 (G) anddepressed (H) to dispense the reaction.

General Features of Devices. In some embodiments, a device of thepresent disclosure can hold 2 or more amplification chambers. In someembodiments, a device of the present disclosure can hold 10 or moredetection chambers. In some embodiments, a device of the presentdisclosure comprises a single chamber in which sample lysis, targetnucleic acid amplification, reverse transcription, and detection are allcarried out. In some cases, different buffers are present in thedifferent chambers. In some embodiments, all the chambers of a device ofthe present disclosure have the same buffer. In some embodiments, thesample chamber comprises the lysis buffer and all of the materials inthe amplification and detection chambers are lyophilized or vitrified.In some embodiments, the sample chamber includes any buffer for lysing asample disclosed herein. The amplification chamber can include anybuffer disclosed herein compatible with amplification and/or reversetranscription of target nucleic acids. The detection chamber can includeany DETECTR or CRISPR buffer (e.g., an MBuffer) disclosed herein orotherwise capable of allowing DETECTR reactions to be carried out. Inthis case, once sample lysing has occurred, volume is moved from thesample chamber to the other chambers in an amount enough to rehydratethe materials in the other chambers. In some embodiments, the devicefurther comprises a pipette pump at one end for aspirating, mixing, anddispensing liquids. In some embodiments, an automated instrument is usedto control aspirating, mixing, and dispensing liquids. In someembodiments, no other instrument is needed for the fluids in the deviceto move from chamber to chamber or for sample mixing to occur. A deviceof the present disclosure may be made of any suitable thermoplastic,such as COC, polymer COP, teflon, or another thermoplastic material.Alternatively, the device may be made of glass. In some embodiments, thedetection chamber may include beads, such as nanoparticles (e.g., a goldnanoparticle). In some embodiments, the reporters are immobilized on thebeads. In some embodiments, after cleavage from the bead, the liberatedreporters flow into a secondary detection chamber, where detection of agenerated signal occurs by any one of the instruments disclosed herein.In some embodiments, the detection chamber is shallow, but has a largesurface area that is optimized for optical detection. A device of thepresent disclosure may also be coupled to a thermoregulator. Forexample, the device may be on top of or adjacent to a planar heater thatcan heat the device up to high temperatures. Alternatively, a metal rodconducting heat is inserted inside the device and presses upon a softpolymer. The heat is transferred to the sample by dissipating throughthe polymer and into the sample. This allows for sample heating withdirect contact between the metal rod and the sample. In someembodiments, in addition to or in place of a buffer for lysing a sample,the sample chamber may include an ultrasonicator for sample lysis. Aswab carrying the sample may be inserted directly into the samplechamber. Commonly, a buccal swab may be used, which can carry blood,urine, or a saliva sample. A filter may be included in any of thechambers in the devices disclosed herein to filter the sample prior tocarrying it to the next step of the method. Any of the devices disclosedherein can be couple to an additional sample preparation module forfurther manipulation of the sample before the various steps of theDETECTR reaction. In some embodiments the reporter can be in solution inthe detection chamber. In other embodiments, the reporter can beimmobilized directly on the surface of the detection chamber. Thesurface can be the top or the bottom of the chamber. In still otherembodiments, the reporter can be immobilized to the surface of a bead.In the case of a bead, after cleavage, the detectable signal may bewashed into a subsequent chamber while the bead remains trapped—thusallowing for separation of the detectable signal from the bead.Alternatively, cleavage of the reporter off of the surface of the beadis enough to generate a strong enough detectable signal to be measured.By sequestering or immobilizing the above described reporters, thestability of the reporters in the devices disclosed herein carrying outDETECTR reactions may be improved. Any of the above devices can becompatible for colorimetric, fluorescence, amperometric, potentiometric,or another electrochemical signal. In some embodiments, thecolorimetric, fluorescence, amperometric, potentiometric, or anotherelectrochemical sign may be detected using a measurement deviceconnected to the detection chamber (e.g., a fluorescence measurementdevice, a spectrophotometer, or an oscilloscope).

In some embodiments, signals themself can be amplified, for example viause of an enzyme such as horse radish peroxidase (HRP). In someembodiments, biotin and avidin reactions, which bind at a 4:1 ratio canbe used to immobilize multiple enzymes or secondary signal molecules(e.g., 4 enzymes of secondary signal molecules, each on a biotin) to asingle protein (e.g., avidin). In some embodiments, an electrochemicalsignal may be produced by an electrochemical molecule (e.g., biotin,ferrocene, digoxigenin, or invertase). In some embodiments, the abovedevices could be couple with an additional concentration step. Forexample, silica membranes may be used to capture nucleic acids off acolumn and directly apply the Cas reaction mixture on top of saidfilter. In some embodiments, the sample chamber of any one of thedevices disclosed herein can hold from 20 ul to 1000 ul of volume. Insome embodiments, the sample chamber holds from 20 to 500, from 40 to400, from 30 to 300, from 20 to 200 or from 10 to 100 ul of volume. Inpreferred embodiments, the sample chamber holds 200 ul of volume. Theamplification and detection chambers can hold a lower volume than thesample chamber. For example, the amplification and detection chambersmay hold from 1 to 50, 10 to 40, 20 to 30, 10 to 40, 5 to 35, 40 to 50,or 1 to 30 ul of volume. Preferrably, the amplification and detectionchambers may hold about 200 ul of volume. In some embodiments, anexonuclease is present in the amplification chamber or may be added tothe amplification chamber. The exonuclease can clean up single strandednucleic acids that are not the target. In some embodiments, primers forthe target nucleic acid can be phosophorothioated in order to preventdegradation of the target nucleic acid in the presence of theexonuclease. In some embodiments, any of the devices disclosed hereincan have a pH balancing well for balancing the pH of a sample. In someembodiments, in each of the above devices, the reporter is present in atleast four-fold excess of total nucleic acids (target nucleicacids+non-target nucleic acids). Preferrably the reporter is present inat least 10-fold excess of total nucleic acids. In some embodiments, thereporter is present in at least 4-fold, at least 5-fold at least 6-fold,at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, atleast 15-fold, at least 20-fold, at least 50-fold, at least 100-fold,from 1.5 to 100-fold, from 4 to 80-fold, from 4 to 10-fold, from 5 to20-fold or from 4 to 15-fold excess of total nucleic acids. In someembodiments, any of the devices disclosed herein can carry out a DETECTRreaction with a limit of detection of at least 0.1 aM, at least 0.1 nM,at least 1 nM or from 0.1 aM to 1 nM. In some embodiments, the devicesdisclosed herein can carry out a DETECTR reaction with a positivepredictive value of at least 75%, at least 80%, at least 85%, at least90%, at least 92%, at least 95%, at least 97%, at least 99%, or 100%. Insome embodiments, the devices disclosed herein can carry out a DETECTRreaction with a negative predictive value of at least 75%, at least 80%,at least 85%, at least 90%, at least 92%, at least 95%, at least 97%, atleast 99%, or 100%. In some embodiments, spatial multiplexing in theabove devices is carried out by having at least one, more than one, orevery detection chamber in the device comprise a unique guide nucleicacid. A unique guide nucleic acid refers to a sequence of a guidenucleic acid that has an at least one nucleotide difference from thesequences of other guide nucleic acids in a plurality of guide nucleicacids, wherein each unique guide nucleic acid of the plurality bind adifferent target nucleic acid. Multiple copies of each unique guidenucleic acid may be present. For example, a unique guide nucleicpopulation may comprise multiple copies of the unique guide nucleicacid.

Support Medium

A number of support mediums are consistent with the devices, systems,fluidic devices, kits, and methods disclosed herein. These supportmediums are, for example, consistent with fluidic devices disclosedherein for detection of a target nucleic acid within the sample, whereinthe fluidic device may comprise multiple pumps, valves, reservoirs, andchambers for sample preparation, amplification of a target nucleic acidwithin the sample, mixing with a programmable nuclease, and detection ofa detectable signal arising from cleavage of detector nucleic acids bythe programmable nuclease within the fluidic system itself. Thesesupport mediums are compatible with the samples, reagents, and fluidicdevices described herein for detection of an ailment, such as a disease,cancer, or genetic disorder, or genetic information, such as forphenotyping, genotyping, or determining ancestry. A support mediumdescribed herein can provide a way to present the results from theactivity between the reagents and the sample. The support mediumprovides a medium to present the detectable signal in a detectableformat. Optionally, the support medium concentrates the detectablesignal to a focused detection area (e.g., a spot, a line, a geometricshape such as a plus sign, or other symbols) in a detection region toincrease the sensitivity, specificity, or accuracy of the assay. Thesupport mediums can present the results of the assay and indicate thepresence or absence of the disease of interest targeted by the targetnucleic acid. The result on the support medium can be read by eye orusing a machine. The support medium helps to stabilize the detectablesignal generated by the cleaved detector molecule on the surface of thesupport medium. In some instances, the support medium is a lateral flowassay strip. In some instances, the support medium is a PCR plate. ThePCR plate can have 96 wells or 384 wells. The PCR plate can have asubset number of wells of a 96 well plate or a 384 well plate. A subsetnumber of wells of a 96 well PCR plate is, for example, 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or 95 wells. Forexample, a PCR subset plate can have 4 wells wherein a well is the sizeof a well from a 96 well PCR plate (e.g., a 4 well PCR subset platewherein the wells are the size of a well from a 96 well PCR plate). Asubset number of wells of a 384 well PCR plate is, for example, 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 30, 32, 35, 40, 45, 50, 55, 60, 64, 65, 70, 75, 80, 85, 90,95, 100, 110, 120, 128, 130, 140, 150, 160, 170, 180, 190, 200, 220,240, 256, 260, 280, 300, 320, 340, 360, or 380 wells. For example, a PCRsubset plate can have 20 wells wherein a well is the size of a well froma 384 well PCR plate (e.g., a 20 well PCR subset plate wherein the wellsare the size of a well from a 384 well PCR plate). The PCR plate or PCRsubset plate can be paired with a fluorescent light reader, a visiblelight reader, or other imaging device. Often, the imaging device is adigital camera, such a digital camera on a mobile device. The mobiledevice may have a software program or a mobile application that cancapture an image of the PCR plate or PCR subset plate, identify theassay being performed, detect the individual wells and the sampletherein, provide image properties of the individuals wells comprisingthe assayed sample, analyze the image properties of the contents of theindividual wells, and provide a result.

The support medium has at least one specialized zone or region topresent the detectable signal. The regions comprise at least one of asample pad region, a nucleic acid amplification region, a conjugate padregion, a detection region, and a collection pad region. In someinstances, the regions are overlapping completely, overlappingpartially, or in series and in contact only at the edges of the regions,where the regions are in fluid communication with its adjacent regions.In some instances, the support medium has a sample pad located upstreamof the other regions; a conjugate pad region having a means forspecifically labeling the detector moiety; a detection region locateddownstream from sample pad; and at least one matrix which defines a flowpath in fluid connection with the sample pad. In some instances, thesupport medium has an extended base layer on top of which the variouszones or regions are placed. The extended base layer may provide amechanical support for the zones.

Described herein are sample pads that provide an area to apply thesample to the support medium. The sample may be applied to the supportmedium by a dropper or a pipette on top of the sample pad, by pouring ordispensing the sample on top of the sample pad region, or by dipping thesample pad into a reagent chamber holding the sample. The sample can beapplied to the sample pad prior to reaction with the reagents when thereagents are placed on the support medium or be reacted with thereagents prior to application on the sample pad. The sample pad regioncan transfer the reacted reagents and sample into the other zones of thesupport medium. Transfer of the reacted reagents and sample may be bycapillary action, diffusion, convection or active transport aided by apump. In some cases, the support medium is integrated with or overlayedby microfluidic channels to facilitate the fluid transport.

The dropper or the pipette may dispense a predetermined volume. In somecases, the predetermined volume may range from about 1 μl to about 1000μl, about 1 μl to about 500 μl, about 1 μl to about 100 μl, or about 1μl to about 50 μl. In some cases, the predetermined volume may be atleast 1 μl, 2 μl, 3 μl, 4 μl, 5 μl, 6 μl, 7 μl, 8 μl, 9 μl, 10 μl, 25μl, 50 μl, 75 μl, 100 μl, 250 μl, 500 μl, 750 μl, or 1000 μl. Thepredetermined volume may be no more than 5 μl, 10 μl, 25 μl, 50 μl, 75μl, 100 μl, 250 μl, 500 μl, 750 μl, or 1000 μl. The predetermined volumemay be from 1 μL to 1000 μL, from 5 μL to 1000 μL, from 10 μL to 1000μL, from 20 μL to 1000 μL, from 50 μL to 1000 μL, from 100 μL to 1000μL, from 200 μL to 1000 μL, from 500 μL to 1000 μL, from 750 μL to 1000μL, from 1 μL to 750 μL, from 5 μL to 750 μL, from 10 μL to 750 μL, from20 μL to 750 μL, from 50 μL to 750 μL, from 100 μL to 750 μL, from 200μL to 750 μL, from 500 μL to 750 μL, from 1 μL to 500 μL, from 5 μL to500 μL, from 10 μL to 500 μL, from 20 μL to 500 μL, from 50 μL to 500μL, from 100 μL to 500 μL, from 200 μL to 500 μL, from 1 μL to 200 μL,from 5 μL to 200 μL, from 10 μL to 200 μL, from 20 μL to 200 μL, from 50μL to 200 μL, from 100 μL to 200 μL, from 1 μL to 100 μL, from 5 μL to100 μL, from 10 μL to 100 μL, from 20 μL to 100 μL, from 50 μL to 100μL, from 1 μL to 50 μL, from 5 μL to 50 μL, from 10 μL to 50 μL, from 20μL to 50 μL, from 1 μL to 20 μL, from 5 μL to 20 μL, from 10 μL to 20μL, from 1 μL to 10 μL, from 5 μL to 10 μL, or from 1 μL to 5 μL. Thedropper or the pipette may be disposable or be single-use.

Optionally, a buffer or a fluid may also be applied to the sample pad tohelp drive the movement of the sample along the support medium. In somecases, the volume of the buffer or the fluid may range from about 1 μlto about 1000 μl, about 1 μl to about 500 μl, about 1 μl to about 100μl, or about 1 μl to about 50 μl. In some cases, the volume of thebuffer or the fluid may be at least 1 μl, 2 μl, 3 μl, 4 μl, 5 μl, 6 μl,7 μl, 8 μl, 9 μl, 10 μl, 25 μl, 50 μl, 75 μl, 100 μl, 250 μl, 500 μl,750 μl, or 1000 μl. The volume of the buffer or the fluid may be no morethan 5 μl, 10 μl, 25 μl, 50 μl, 75 μl, 100 μl, 250 μl, 500 μl, 750 μl,or 1000 μl. In some cases, the volume of the buffer or the fluid may befrom 1 μL to 1000 μL, from 5 μL to 1000 μL, from 10 μL to 1000 μL, from20 μL to 1000 μL, from 50 μL to 1000 μL, from 100 μL to 1000 μL, from200 μL to 1000 μL, from 500 μL to 1000 μL, from 750 μL to 1000 μL, from1 μL to 750 μL, from 5 μL to 750 μL, from 10 μL to 750 μL, from 20 μL to750 μL, from 50 μL to 750 μL, from 100 μL to 750 μL, from 200 μL to 750μL, from 500 μL to 750 μL, from 1 μL to 500 μL, from 5 μL to 500 μL,from 10 μL to 500 μL, from 20 μL to 500 μL, from 50 μL to 500 μL, from100 μL to 500 μL, from 200 μL to 500 μL, from 1 μL to 200 μL, from 5 μLto 200 μL, from 10 μL to 200 μL, from 20 μL to 200 μL, from 50 μL to 200μL, from 100 μL to 200 μL, from 1 μL to 100 μL, from 5 μL to 100 μL,from 10 μL to 100 μL, from 20 μL to 100 μL, from 50 μL to 100 μL, from 1μL to 50 μL, from 5 μL to 50 μL, from 10 μL to 50 μL, from 20 μL to 50μL, from 1 μL to 20 μL, from 5 μL to 20 μL, from 10 μL to 20 μL, from 1μL to 10 μL, from 5 μL to 10 μL, or from 1 μL to 5 μL. In some cases,the buffer or fluid may have a ratio of the sample to the buffer orfluid of at least 1:1, 1:2, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9, or 1:10.

The sample pad can be made from various materials that transfer most ofthe applied reacted reagents and samples to the subsequent regions. Thesample pad may comprise cellulose fiber filters, woven meshes, porousplastic membranes, glass fiber filters, aluminum oxide coated membranes,nitrocellulose, paper, polyester filter, or polymer-based matrices. Thematerial for the sample pad region may be hydrophilic and have lownon-specific binding. The material for the sample pad may range fromabout 50 μm to about 1000 μm, about 50 μm to about 750 μm, about 50 μmto about 500 μm, or about 100 μm to about 500 μm. In some cases thematerial for the sample pad may range from about 50 μm to about 1000 μm,from about 75 μm to about 1000 μm, from about 100 μm to about 1000 μm,from about 200 μm to about 1000 μm, from about 500 μm to about 1000 μm,from about 750 μm to about 1000 μm, from about 50 μm to about 750 μm,from about 75 μm to about 750 μm, from about 100 μm to about 750 μm,from about 200 μm to about 750 μm, from about 500 μm to about 750 μm,from about 50 μm to about 500 μm, from about 75 μm to about 500 μm, fromabout 100 μm to about 500 μm, from about 200 μm to about 500 μm, fromabout 50 μm to about 200 μm, from about 75 μm to about 200 μm, fromabout 100 μm to about 200 μm, from about 50 μm to about 100 μm, fromabout 75 μm to about 100 μm, or from about 50 μm to about 75 μm.

The sample pad can be treated with chemicals to improve the presentationof the reaction results on the support medium. The sample pad can betreated to enhance extraction of nucleic acid in the sample, to controlthe transport of the reacted reagents and sample or the conjugate toother regions of the support medium, or to enhance the binding of thecleaved detection moiety to the conjugate binding molecule on thesurface of the conjugate or to the capture molecule in the detectionregion. The chemicals may comprise detergents, surfactants, buffers,salts, viscosity enhancers, or polypeptides. In some instances, thechemical comprises bovine serum albumin.

Described herein are conjugate pads that provide a region on the supportmedium comprising conjugates coated on its surface by conjugate bindingmolecules that can bind to the detector moiety from the cleaved detectormolecule or to the control molecule. The conjugate pad can be made fromvarious materials that facilitate binding of the conjugate bindingmolecule to the detection moiety from cleaved detector molecule andtransfer of most of the conjugate-bound detection moiety to thesubsequent regions. The conjugate pad may comprise the same material asthe sample pad or other zones or a different material than the samplepad. The conjugate pad may comprise glass fiber filters, porous plasticmembranes, aluminum oxide coated membranes, paper, cellulose fiberfilters, woven meshes, polyester filter, or polymer-based matrices. Thematerial for the conjugate pad region may be hydrophilic, have lownon-specific binding, or have consistent fluid flow properties acrossthe conjugate pad. In some cases, the material for the conjugate pad mayrange from about 50 μm to about 1000 μm, about 50 μm to about 750 μm,about 50 μm to about 500 μm, or about 100 μm to about 500 μm. In somecases, the material for the conjugate pad may range from about 50 μm toabout 1000 μm, from about 75 μm to about 1000 μm, from about 100 μm toabout 1000 μm, from about 200 μm to about 1000 μm, from about 500 μm toabout 1000 μm, from about 750 μm to about 1000 μm, from about 50 μm toabout 750 μm, from about 75 μm to about 750 μm, from about 100 μm toabout 750 μm, from about 200 μm to about 750 μm, from about 500 μm toabout 750 μm, from about 50 μm to about 500 μm, from about 75 μm toabout 500 μm, from about 100 μm to about 500 μm, from about 200 μm toabout 500 μm, from about 50 μm to about 200 μm, from about 75 μm toabout 200 μm, from about 100 μm to about 200 μm, from about 50 μm toabout 100 μm, from about 75 μm to about 100 μm, or from about 50 μm toabout 75 μm.

Further described herein are conjugates that are placed on the conjugatepad and immobilized to the conjugate pad until the sample is applied tothe support medium. The conjugates may comprise a nanoparticle, a goldnanoparticle, a latex nanoparticle, a quantum dot, a chemiluminescentnanoparticle, a carbon nanoparticle, a selenium nanoparticle, afluorescent nanoparticle, a liposome, or a dendrimer. The surface of theconjugate may be coated by a conjugate binding molecule that binds tothe detection moiety from the cleaved detector molecule.

The conjugate binding molecules described herein coat the surface of theconjugates and can bind to detection moiety. The conjugate bindingmolecule binds selectively to the detection moiety cleaved from thedetector nucleic acid. Some suitable conjugate binding moleculescomprise an antibody, a polypeptide, or a single stranded nucleic acid.In some cases, the conjugate binding molecule binds a dye and afluorophore. Some such conjugate binding molecules that bind to a dye ora fluorophore can quench their signal. In some cases, the conjugatebinding molecule is a monoclonal antibody. In some cases, an antibody,also referred to as an immunoglobulin, includes any isotype, variableregions, constant regions, Fc region, Fab fragments, F(ab′)2 fragments,and Fab′ fragments. Alternatively, the conjugate binding molecule is anon-antibody compound that specifically binds the detection moiety.Sometimes, the conjugate binding molecule is a polypeptide that can bindto the detection moiety. Sometimes, the conjugate binding molecule isavidin or a polypeptide that binds biotin. Sometimes, the conjugatebinding molecule is a detector moiety binding nucleic acid.

The diameter of the conjugate may be selected to provide a desiredsurface to volume ratio. In some instances, a high surface area tovolume ratio may allow for more conjugate binding molecules that areavailable to bind to the detection moiety per total volume of theconjugates. In some cases, the diameter of the conjugate may range fromabout 1 nm to about 1000 nm, about 1 nm to about 500 nm, about 1 nm toabout 100 nm, or about 1 nm to about 50 nm. In some cases, the diameterof the conjugate may range from about 2 nm to about 500 nm, from about 5nm to about 200 nm, from about 10 nm to about 200 nm, or from about 20nm to about 50 nm. In some cases, the diameter of the conjugate mayrange from about 1 nm to about 500 nm, from about 10 nm to about 500 nm,from about 100 nm to about 500 nm, from about 200 nm to about 500 nm,from about 300 nm to about 500 nm, from about 1 nm to about 300 nm, fromabout 10 nm to about 300 nm, from about 100 nm to about 300 nm, fromabout 200 nm to about 300 nm, from about 1 nm to about 200 nm, fromabout 10 nm to about 200 nm, from about 100 nm to about 200 nm, fromabout 1 nm to about 100 nm, from about 10 nm to about 100 nm, or fromabout 1 nm to about 10 nm. In some cases, the diameter of the conjugatemay be at least 1 nm, 2 nm, 3 nm, 4 nm, 5 nm, 6 nm, 7 nm, 8 nm, 9 nm, 10nm, 15 nm, 20 nm, 25 nm, 30 nm, 30 nm, 35 nm, 40 nm, 45 nm, 50 nm, 55nm, 60 nm, 65 nm, 70 nm, 75 nm, 80 nm, 85 nm, 90 nm, 95 nm, 100 nm, 200nm, 300 nm, 400 nm, 500 nm, 600 nm, 700 nm, 800 nm, 900 nm, or 1000 nm.In some cases, the diameter of the conjugate may be no more than 1 nm, 2nm, 3 nm, 4 nm, 5 nm, 6 nm, 7 nm, 8 nm, 9 nm, 10 nm, 15 nm, 20 nm, 25nm, 30 nm, 30 nm, 35 nm, 40 nm, 45 nm, 50 nm, 55 nm, 60 nm, 65 nm, 70nm, 75 nm, 80 nm, 85 nm, 90 nm, 95 nm, 100 nm, 200 nm, 300 nm, 400 nm,500 nm, 600 nm, 700 nm, 800 nm, 900 nm, or 1000 nm.

The ratio of conjugate binding molecules to the conjugates can betailored to achieve desired binding properties between the conjugatebinding molecules and the detection moiety. In some instances, the molarratio of conjugate binding molecules to the conjugates is at least 1:1,1:5, 1:10, 1:20, 1:30, 1:40, 1:50, 1:60, 1:70, 1:80, 1:90, 1:100, 1:110,1:120, 1:130, 1:140, 1:150, 1:160, 1:170, 1:180, 1:190, 1:200, 1:250,1:300, 1:350, 1:400, 1:450, or 1:500. In some instances, the mass ratioof conjugate binding molecules to the conjugates is at least 1:1, 1:5,1:10, 1:20, 1:30, 1:40, 1:50, 1:60, 1:70, 1:80, 1:90, 1:100, 1:110,1:120, 1:130, 1:140, 1:150, 1:160, 1:170, 1:180, 1:190, 1:200, 1:250,1:300, 1:350, 1:400, 1:450, or 1:500. In some instances, the number ofconjugate binding molecules per conjugate is at least 1, 10, 50, 100,500, 1000, 5000, or 10000.

The conjugate binding molecules can be bound to the conjugates byvarious approaches. Sometimes, the conjugate binding molecule can bebound to the conjugate by passive binding. Some such passive bindingcomprise adsorption, absorption, hydrophobic interaction, electrostaticinteraction, ionic binding, or surface interactions. In some cases, theconjugate binding molecule can be bound to the conjugate covalently.Sometimes, the covalent bonding of the conjugate binding molecule to theconjugate is facilitated by EDC/NHS chemistry or thiol chemistry.

Described herein are detection regions on the support medium thatprovide a region for presenting the assay results. The detection regioncan be made from various materials that facilitate binding of theconjugate-bound detection moiety from cleaved detector molecule to thecapture molecule specific for the detection moiety. The detection padmay comprise the same material as other zones or a different materialthan the other zones. The detection region may comprise nitrocellulose,paper, cellulose, cellulose fiber filters, glass fiber filters, porousplastic membranes, aluminum oxide coated membranes, woven meshes,polyester filter, or polymer-based matrices. Often the detection regionmay comprise nitrocellulose. The material for the region pad region maybe hydrophilic, have low non-specific binding, or have consistent fluidflow properties across the region pad. The material for the conjugatepad may range from about 10 μm to about 1000 μm, about 10 μm to about750 μm, about 10 μm to about 500 μm, or about 10 μm to about 300 μm. Insome cases, the material for the conjugate pad may range from about 50μm to about 1000 μm, from about 75 μm to about 1000 μm, from about 100μm to about 1000 μm, from about 200 μm to about 1000 μm, from about 500μm to about 1000 μm, from about 750 μm to about 1000 μm, from about 50μm to about 750 μm, from about 75 μm to about 750 μm, from about 100 μmto about 750 μm, from about 200 μm to about 750 μm, from about 500 μm toabout 750 μm, from about 50 μm to about 500 μm, from about 75 μm toabout 500 μm, from about 100 μm to about 500 μm, from about 200 μm toabout 500 μm, from about 50 μm to about 200 μm, from about 75 μm toabout 200 μm, from about 100 μm to about 200 μm, from about 50 μm toabout 100 μm, from about 75 μm to about 100 μm, or from about 50 μm toabout 75 μm.

The detection region comprises at least one capture area with a highdensity of a capture molecule that can bind to the detection moiety fromcleaved detection molecule and at least one area with a high density ofa positive control capture molecule. The capture area with a highdensity of capture molecule or a positive control capture molecule maybe a line, a circle, an oval, a rectangle, a triangle, a plus sign, orany other shapes. In some instances, the detection region comprise morethan one capture area with high densities of more than one capturemolecules, where each capture area comprises one type of capturemolecule that specifically binds to one type of detection moiety fromcleaved detection molecule and are different from the capture moleculesin the other capture areas. The capture areas with different capturemolecules may be overlapping completely, overlapping partially, orspatially separate from each other. In some instances, the capture areasmay overlap and produce a combined detectable signal distinct from thedetectable signals generated by the individual capture areas. Usually,the positive control spot is spatially distinct from any of thedetection spot.

The capture molecules described herein can bind to a detection moietyand can be immobilized in the detection area in the detect region. Somesuitable capture molecules comprise an antibody, a polypeptide, or asingle stranded nucleic acid. In some cases, the capture molecule bindsa dye and a fluorophore. Some such capture molecules that bind to a dyeor a fluorophore can quench their signal. Sometimes, the capturemolecule is an antibody that binds to a dye or a fluorophore. In somecases, the capture molecule is a monoclonal antibody. In some cases, anantibody, also referred to as an immunoglobulin, includes any isotype,variable regions, constant regions, Fc region, Fab fragments, F(ab′)2fragments, and Fab′ fragments. Alternatively, the capture molecule is anon-antibody compound that specifically binds the detection moiety.Sometimes, the capture molecule is a polypeptide that can bind to thedetection moiety. In some instances, the detection moiety from cleaveddetection molecule has a conjugate bound to the detection moiety, andthe conjugate-detection moiety complex may bind to the capture moleculespecific to the detection moiety on the detection region. Sometimes, thecapture molecule is a polypeptide that can bind to the detection moiety.Sometimes, the capture molecule is avidin or a polypeptide that bindsbiotin. Sometimes, the capture molecule is a detector moiety bindingnucleic acid.

The detection region described herein comprises at least one area with ahigh density of a positive control capture molecule. The positivecontrol spot in the detection region provides a validation of the assayand a confirmation of completion of the assay. If the positive controlspot is not detectable by the visualization methods described herein,the assay is not valid and should be performed again with a new systemor kit. The positive control capture molecule binds at least one of theconjugate, the conjugate binding molecule, or detection moiety and isimmobilized in the positive control spot in the detect region. Somesuitable positive control capture molecules comprise an antibody, apolypeptide, or a single stranded nucleic acid. In some cases, thepositive control capture molecule binds to the conjugate bindingmolecule. Some such positive control capture molecules that bind to adye or a fluorophore can quench their signal. Sometimes, the positivecontrol capture molecule is an antibody that binds to a dye or afluorophore. In some cases, the positive control capture molecule is amonoclonal antibody. In some cases, an antibody includes any isotype,variable regions, constant regions, Fc region, Fab fragments, F(ab′)2fragments, and Fab′ fragments. Alternatively, the positive controlcapture molecule is a non-antibody compound that specifically binds thedetection moiety. Sometimes, the positive control capture molecule is apolypeptide that can bind to at least one of the conjugate, theconjugate binding molecule, or detection moiety. In some instances, theconjugate unbound to the detection moiety binds to the positive controlcapture molecule specific to at least one of the conjugate, theconjugate binding molecule.

Housing

A support medium as described herein can be housed in a number of waysthat are consistent with the devices, systems, fluidic devices, kits,and methods disclosed herein. The housing for the support medium are,for example, consistent with fluidic devices disclosed herein fordetection of a target nucleic acid within the sample, wherein thefluidic device may comprise multiple pumps, valves, reservoirs, andchambers for sample preparation, amplification of a target nucleic acidwithin the sample, mixing with a programmable nuclease, and detection ofa detectable signal arising from cleavage of detector nucleic acids bythe programmable nuclease within the fluidic system itself. For example,the fluidic device may be comprise support mediums to channel the flowof fluid from one chamber to another and wherein the entire fluidicdevice is encased within the housing described herein. Typically, thesupport medium described herein is encased in a housing to protect thesupport medium from contamination and from disassembly. The housing canbe made of more than one part and assembled to encase the supportmedium. In some instances, a single housing can encase more than onesupport medium. The housing can be made from cardboard, plastics,polymers, or materials that provide mechanical protection for thesupport medium. Often, the material for the housing is inert or does notreact with the support medium or the reagents placed on the supportmedium. The housing may have an upper part which when in place exposesthe sample pad to receive the sample and has an opening or window abovethe detection region to allow the results of the lateral flow assay tobe read. The housing may have guide pins on its inner surface that areplaced around and on the support medium to help secure the compartmentsand the support medium in place within the housing. In some cases, thehousing encases the entire support medium. Alternatively, the sample padof the support medium is not encased and is left exposed to facilitatethe receiving of the sample while the rest of the support medium isencased in the housing.

The housing and the support medium encased within the housing may besized to be small, portable, and hand held. The small size of thehousing and the support medium would facilitate the transport and use ofthe assay in remote regions or low resource settings. In some cases, thehousing has a length of no more than 30 cm, 25 cm, 20 cm, 15 cm, 10 cm,or 5 cm. In some cases, the housing has a length of at least 1 cm, 5 cm,10 cm, 15 cm, 20 cm, 25 cm, or 30 cm. In some cases the housing has alength of from 1 cm to 30 cm, from 5 cm to 30 cm, from 10 cm to 30 cm,from 15 cm to 30 cm, from 20 cm to 30 cm, from 25 cm to 30 cm, from 1 cmto 25 cm, from 5 cm to 25 cm, from 10 cm to 25 cm, from 15 cm to 25 cm,from 20 cm to 25 cm, from 1 cm to 20 cm, from 5 cm to 20 cm, from 10 cmto 20 cm, from 15 cm to 20 cm, from 1 cm to 15 cm, from 5 cm to 15 cm,from 10 cm to 15 cm, from 1 cm to 10 cm, from 5 cm to 10 cm, or from 1cm to 5 cm. In some cases, the housing has a width of no more than 30cm, 25 cm, 20 cm, 15 cm, 10 cm, 5 cm, 4 cm, 3 cm, 2 cm, or 1 cm. In somecases, the housing has a width of at least 1 cm, 2 cm, 3 cm, 4 cm, 5 cm,10 cm, 15 cm, 20 cm, 25 cm, or 30 cm. In some cases the housing has awidth of from 1 cm to 30 cm, from 5 cm to 30 cm, from 10 cm to 30 cm,from 15 cm to 30 cm, from 20 cm to 30 cm, from 25 cm to 30 cm, from 1 cmto 25 cm, from 5 cm to 25 cm, from 10 cm to 25 cm, from 15 cm to 25 cm,from 20 cm to 25 cm, from 1 cm to 20 cm, from 5 cm to 20 cm, from 10 cmto 20 cm, from 15 cm to 20 cm, from 1 cm to 15 cm, from 5 cm to 15 cm,from 10 cm to 15 cm, from 1 cm to 10 cm, from 5 cm to 10 cm, or from 1cm to 5 cm. In some cases, the housing has a height of no more than 10cm, 9 cm, 8 cm, 7 cm, 6 cm, 5 cm, 4 cm, 3 cm, 2 cm, or 1 cm. In somecases, the housing has a height of at least 1 cm, 2 cm, 3 cm, 4 cm, 5cm, 6 cm, 7 cm, 8 cm, 9 cm, or 10 cm. In some cases the housing has aheight of from from 1 cm to 30 cm, from 5 cm to 30 cm, from 10 cm to 30cm, from 15 cm to 30 cm, from 20 cm to 30 cm, from 25 cm to 30 cm, from1 cm to 25 cm, from 5 cm to 25 cm, from 10 cm to 25 cm, from 15 cm to 25cm, from 20 cm to 25 cm, from 1 cm to 20 cm, from 5 cm to 20 cm, from 10cm to 20 cm, from 15 cm to 20 cm, from 1 cm to 15 cm, from 5 cm to 15cm, from 10 cm to 15 cm, from 1 cm to 10 cm, from 5 cm to 10 cm, or from1 cm to 5 cm. Typically, the housing is rectangular in shape.

In some instances, the housing provides additional information on theouter surface of the upper cover to facilitate the identification of thetest type, visualization of the detection region, and analysis of theresults. The upper outer housing may have identification label includingbut not limited to barcodes, QR codes, identification label, or othervisually identifiable labels. In some instances, the identificationlabel is imaged by a camera on a mobile device, and the image isanalyzed to identify the disease, cancer, or genetic disorder that isbeing tested for. The correct identification of the test is important toaccurately visualize and analyze the results. In some instances, theupper outer housing has fiduciary markers to orient the detection regionto distinguish the positive control spot from the detection spots. Insome instances, the upper outer housing has a color reference guide.When the detection region is imaged with the color reference guide, thedetection spots, located using the fiduciary marker, can be comparedwith the positive control spot and the color reference guide todetermine various image properties of the detection spot such as color,color intensity, and size of the spot. In some instances, the colorreference guide has red, green, blue, black, and white colors. In somecases, the image of the detection spot can be normalized to at least oneof the reference colors of the color reference guide, compared to atleast two of the reference colors of the color reference guide, andgenerate a value for the detection spot. Sometimes, the comparison to atleast two of the reference colors is comparison to a standard referencescale. In some instance, the image of the detection spot in someinstance undergoes transformation or filtering prior to analysis.Analysis of the image properties of the detection spot can provideinformation regarding presence or absence of the target nucleic acidtargeted by the assay and the disease, cancer, or genetic disorderassociated with the target nucleic acid. In some instances, the analysisprovides a qualitative result of presence or absence of the targetnucleic acid in the sample. In some instances, the analysis provides asemi-quantitative or quantitative result of the level of the targetnucleic acid present in the sample. Quantification may be performed byhaving a set of standards in spots/wells and comparing the test sampleto the range of standards. A more semi-quantitative approach may beperformed by calculating the color intensity of 2 spots/well compared toeach other and measuring if one spot/well is more intense than theother. Sometimes, quantification is of quantification of circulatingnucleic acid. The circulating nucleic acid can comprise a target nucleicacid. For example, a method of circulating nucleic acid quantificationcomprises assaying for a target nucleic acid of circulating nucleic acidin a first aliquot of a sample, assaying for a control nucleic acid in asecond aliquot of the sample, and quantifying the target nucleic acidtarget in the first aliquot by measuring a signal produced by cleavageof a detector nucleic acid. Sometimes, a method of circulating RNAquantification comprises assaying for a target nucleic acid of thecirculating RNA in a first aliquot of a sample, assaying for a controlnucleic acid in a second aliquot of the sample, and quantifying thetarget nucleic acid target in the first aliquot by measuring a signalproduced by cleavage of a detector nucleic acid. Often, the outputcomprises fluorescence/second. The reaction rate, sometimes, is loglinear for output signal and target nucleic acid concentration. In someinstances, the signal output is correlated with the target nucleic acidconcentration. Sometimes, the circulating nucleic acid is DNA.

Detection/Visualization Devices

A number of detection or visualization devices and methods areconsistent with the devices, systems, fluidic devices, kits, and methodsdisclosed herein. Methods of detection/visualization are, for example,consistent with fluidic devices disclosed herein for detection of atarget nucleic acid within the sample, wherein the fluidic device maycomprise multiple pumps, valves, reservoirs, and chambers for samplepreparation, amplification of a target nucleic acid within the sample,mixing with a programmable nuclease, and detection of a detectablesignal arising from cleavage of detector nucleic acids by theprogrammable nuclease within the fluidic system itself. For example, thefluidic device may comprise an incubation and detection chamber or astand-alone detection chamber, in which a colorimetric, fluorescence,electrochemical, or electrochemiluminesence signal is generated fordetection/visualization. Sometimes, the signal generated for detectionis a calorimetric, potentiometric, amperometric, optical (e.g.,fluorescent, colorometric, etc.), or piezo-electric signal. Often acalorimetric signal is heat produced after cleavage of the detectornucleic acids. Sometimes, a calorimetric signal is heat absorbed aftercleavage of the detector nucleic acids. A potentiometric signal, forexample, is electrical potential produced after cleavage of the detectornucleic acids. An amperometric signal can be movement of electronsproduced after the cleavage of detector nucleic acid. Often, the signalis an optical signal, such as a colorometric signal or a fluorescencesignal. An optical signal is, for example, a light output produced afterthe cleavage of the detector nucleic acids. Sometimes, an optical signalis a change in light absorbance between before and after the cleavage ofdetector nucleic acids. Often, a piezo-electric signal is a change inmass between before and after the cleavage of the detector nucleic acid.Sometimes, the detector nucleic acid is protein-nucleic acid. Often, theprotein-nucleic acid is an enzyme-nucleic acid. Thedetection/visualization can be analyzed using various methods, asfurther described below. The results from the detection region from acompleted assay can be visualized and analyzed in various ways. In somecases, the positive control spot and the detection spot in the detectionregion is visible by eye, and the results can be read by the user. Insome cases, the positive control spot and the detection spot in thedetection region is visualized by an imaging device. Often, the imagingdevice is a digital camera, such a digital camera on a mobile device.The mobile device may have a software program or a mobile applicationthat can capture an image of the support medium, identify the assaybeing performed, detect the detection region and the detection spot,provide image properties of the detection spot, analyze the imageproperties of the detection spot, and provide a result. Alternatively orin combination, the imaging device can capture fluorescence, ultraviolet(UV), infrared (IR), or visible wavelength signals. The imaging devicemay have an excitation source to provide the excitation energy andcaptures the emitted signals. In some cases, the excitation source canbe a camera flash and optionally a filter. In some cases, the imagingdevice is used together with an imaging box that is placed over thesupport medium to create a dark room to improve imaging. The imaging boxcan be a cardboard box that the imaging device can fit into beforeimaging. In some instances, the imaging box has optical lenses, mirrors,filters, or other optical elements to aid in generating a more focusedexcitation signal or to capture a more focused emission signal. Often,the imaging box and the imaging device are small, handheld, and portableto facilitate the transport and use of the assay in remote or lowresource settings.

The assay described herein can be visualized and analyzed by a mobileapplication (app) or a software program. Using the graphic userinterface (GUI) of the app or program, an individual can take an imageof the support medium, including the detection region, barcode,reference color scale, and fiduciary markers on the housing, using acamera on a mobile device. The program or app reads the barcode oridentifiable label for the test type, locate the fiduciary marker toorient the sample, and read the detectable signals, compare against thereference color grid, and determine the presence or absence of thetarget nucleic acid, which indicates the presence of the gene, virus, orthe agent responsible for the disease, cancer, or genetic disorder. Themobile application can present the results of the test to theindividual. The mobile application can store the test results in themobile application. The mobile application can communicate with a remotedevice and transfer the data of the test results. The test results canbe viewable remotely from the remote device by another individual,including a healthcare professional. A remote user can access theresults and use the information to recommend action for treatment,intervention, clean up of an environment.

Manufacturing

The support medium may be assembled with a variety of materials andreagents. Reagents may be dispensed or coated on to the surface of thematerial for the support medium. The material for the support medium maybe laminated to a backing card, and the backing card may be singulatedor cut into individual test strips. The device may be manufactured bycompletely manual, batch-style processing; or a completely automated,in-line continuous process; or a hybrid of the two processingapproaches. The batch process may start with sheets or rolls of eachmaterial for the support medium. Individual zones of the support mediummay be processed independently for dispensing and drying, and the finalsupport medium may be assembled with the independently prepared zonesand cut. The batch processing scheme may have a lower cost of equipment,and a higher labor cost than more automated in-line processing, whichmay have higher equipment costs. In some instances, batch processing maybe preferred for low volume production due to the reduced capitalinvestment. In some instances, automated in-line processing may bepreferred for high volume production due to reduced production time.Both approaches may be scalable to production level.

In some instances, the support mediums are prepared using variousinstruments, including an XYZ-direction motion system with dispensers,impregnation tanks, drying ovens, a manual or semi-automated laminator,and cutting methods for reducing roll or sheet stock to appropriatelengths and widths for lamination. For dispensing the conjugate bindingmolecules for the conjugate zone and capture molecules for the detectionzones, an XYZ-direction motion system with dispensers may be used. Insome embodiments, the dispenser may dispense by a contact method or anon-contact method.

In automated or semi-automated preparation of the support medium, thesupport medium may be prepared from rolls of membranes for each regionthat are ordered into the final assembled order and unfurled from therolls. For example, the membranes can be ordered from sample pad regionto collection pad region from left to right with one membranecorresponding to a region on the support medium, all onto an adhesivecardstock. The dispenser places the reagents, conjugates, detectionmolecules, and other treatments for the membrane onto the membrane. Thedispensed fluids are dried onto the membranes by heat, in a low humiditychamber, or by freeze drying to stabilize the dispensed molecules. Themembranes are cut into strips and placed into the housing and packaged.

Kits for Assays

A number of kits are consistent with the devices, systems, fluidicdevices, kits, and methods disclosed herein for performing the assays asdescribed herein. For example, the kits for assays as disclosed hereincan be used to detect a target nucleic acid. These kits are, forexample, consistent with fluidic devices disclosed herein for detectionof a target nucleic acid within the sample, wherein the fluidic devicemay comprise multiple pumps, valves, reservoirs, and chambers for samplepreparation, amplification of a target nucleic acid within the sample,mixing with a programmable nuclease, and detection of a detectablesignal arising from cleavage of detector nucleic acids by theprogrammable nuclease within the fluidic system itself. In someembodiments, the kit comprises the reagents and the support medium. Thereagent may be provided in a reagent chamber or on the support medium.Alternatively, the reagent may be placed into the reagent chamber or thesupport medium by the individual using the kit. Optionally, the kitfurther comprises a buffer and a dropper. The reagent chamber be a testwell or container. The opening of the reagent chamber may be largeenough to accommodate the support medium. The buffer may be provided ina dropper bottle for ease of dispensing. The dropper can be disposableand transfer a fixed volume. The dropper can be used to place a sampleinto the reagent chamber or on the support medium.

In some embodiments, a kit for detecting a target nucleic acidcomprising a support medium; a guide nucleic acid targeting a targetnucleic acid segment; a programmable nuclease capable of being activatedwhen complexed with the guide nucleic acid and the target nucleic acidsegment; and a single stranded detector nucleic acid comprising adetection moiety, wherein the detector nucleic acid is capable of beingcleaved by the activated nuclease, thereby generating a first detectablesignal.

In some embodiments, a kit for detecting a target nucleic acidcomprising a PCR plate; a guide nucleic acid targeting a target nucleicacid segment; a programmable nuclease capable of being activated whencomplexed with the guide nucleic acid and the target nucleic acidsegment; and a single stranded detector nucleic acid comprising adetection moiety, wherein the detector nucleic acid is capable of beingcleaved by the activated nuclease, thereby generating a first detectablesignal. The wells of the PCR plate can be pre-aliquoted with the guidenucleic acid targeting a target nucleic acid segment, a programmablenuclease capable of being activated when complexed with the guidenucleic acid and the target sequence, and at least one population of asingle stranded detector nucleic acid comprising a detection moiety. Auser can thus add the biological sample of interest to a well of thepre-aliquoted PCR plate and measure for the detectable signal with afluorescent light reader or a visible light reader.

In some instances, such kits may include a package, carrier, orcontainer that is compartmentalized to receive one or more containerssuch as vials, tubes, and the like, each of the container(s) comprisingone of the separate elements to be used in a method described herein.Suitable containers include, for example, test wells, bottles, vials,and test tubes. In one embodiment, the containers are formed from avariety of materials such as glass, plastic, or polymers.

The kit or systems described herein contain packaging materials.Examples of packaging materials include, but are not limited to,pouches, blister packs, bottles, tubes, bags, containers, bottles, andany packaging material suitable for intended mode of use.

A kit typically includes labels listing contents and/or instructions foruse, and package inserts with instructions for use. A set ofinstructions will also typically be included. In one embodiment, a labelis on or associated with the container. In some instances, a label is ona container when letters, numbers or other characters forming the labelare attached, molded or etched into the container itself; a label isassociated with a container when it is present within a receptacle orcarrier that also holds the container, e.g., as a package insert. In oneembodiment, a label is used to indicate that the contents are to be usedfor a specific therapeutic application. The label also indicatesdirections for use of the contents, such as in the methods describedherein.

After packaging the formed product and wrapping or boxing to maintain asterile barrier, the product may be terminally sterilized by heatsterilization, gas sterilization, gamma irradiation, or by electron beamsterilization. Alternatively, the product may be prepared and packagedby aseptic processing.

Reagent Kits

Described herein is a kit comprising the reagents as disclosed hereinfor detecting a target nucleic acid. These reagent kits are, forexample, consistent with fluidic devices disclosed herein for detectionof a target nucleic acid within the sample, wherein the fluidic devicemay comprise multiple pumps, valves, reservoirs, and chambers for samplepreparation, amplification of a target nucleic acid within the sample,mixing with a programmable nuclease, and detection of a detectablesignal arising from cleavage of detector nucleic acids by theprogrammable nuclease within the fluidic system itself. The kit maycomprise a support medium; a guide nucleic acid targeting a targetsequence; a programmable nuclease capable of being activated whencomplexed with the guide nucleic acid and the target sequence; and asingle stranded detector nucleic acid comprising a detection moiety,wherein the detector nucleic acid is capable of being cleaved by theactivated nuclease, thereby generating a first detectable signal. Thekits described herein may be used for detecting in a biological samplethe presence or absence of a target nucleic acid. The kit or systemdescribed herein may also comprise a positive control sample todetermine that the activity of at least one of programmable nuclease, aguide nucleic acid, or a single stranded detector nucleic acid. Often,the positive control sample comprises a target nucleic acid that bindsto the guide nucleic acid. The positive control sample is contacted withthe reagents in the same manner as the test sample and visualized usingthe support medium. The visualization of the positive control spot andthe detection spot for the positive control sample provides a validationof the reagents and the assay.

The kit or system for detection of a target nucleic acid describedherein further can comprise reagents for protease treatment of thesample. The sample can be treated with protease, such as Proteinase K,before amplification or before assaying for a detectable signal. Often,a protease treatment is for no more than 15 minutes. Sometimes, theprotease treatment is for no more than 1, 5, 10, 15, 20, 25, 30, or moreminutes, or any value from 1 to 30 minutes. Sometimes, the proteasetreatment is from 1 minute to 30 minutes, from 5 minutes to 30 minutes,from 10 minutes to 30 minutes, from 15 minutes to 30 minutes, from 20minutes to 30 minutes, from 25 minutes to 30 minutes, from 1 minute to25 minutes, from 5 minutes to 25 minutes, from 10 minutes to 25 minutes,from 15 minutes to 25 minutes, from 20 minutes to 25 minutes, from 1minute to 20 minutes, from 5 minutes to 20 minutes, from 10 minutes to20 minutes, from 15 minutes to 20 minutes, from 1 minute to 15 minutes,from 5 minutes to 15 minutes, from 10 minutes to 15 minutes, from 1minute to 10 minutes, from 5 minutes to 10 minutes, or from 1 minute to5 minutes.

The kit or system for detection of a target nucleic acid describedherein further comprises reagents for nucleic acid amplification oftarget nucleic acids in the sample. Isothermal nucleic acidamplification allows the use of the kit or system in remote regions orlow resource settings without specialized equipment for amplification.Often, the reagents for nucleic acid amplification comprise arecombinase, an oligonucleotide primer, a single-stranded DNA binding(SSB) protein, and a polymerase. Sometimes, nucleic acid amplificationof the sample improves at least one of sensitivity, specificity, oraccuracy of the assay in detecting the target nucleic acid. In somecases, the nucleic acid amplification is performed in a nucleic acidamplification region on the support medium. Alternatively or incombination, the nucleic acid amplification is performed in a reagentchamber, and the resulting sample is applied to the support medium.Sometimes, the nucleic acid amplification is isothermal nucleic acidamplification. In some cases, the nucleic acid amplification istranscription mediated amplification (TMA). Nucleic acid amplificationis helicase dependent amplification (HDA) or circular helicase dependentamplification (cHDA) in other cases. In additional cases, nucleic acidamplification is strand displacement amplification (SDA). In some cases,nucleic acid amplification is by recombinase polymerase amplification(RPA). In some cases, nucleic acid amplification is by at least one ofloop mediated amplification (LAMP) or the exponential amplificationreaction (EXPAR). Nucleic acid amplification is, in some cases, byrolling circle amplification (RCA), ligase chain reaction (LCR), simplemethod amplifying RNA targets (SMART), single primer isothermalamplification (SPIA), multiple displacement amplification (MDA), nucleicacid sequence based amplification (NASBA), hinge-initiatedprimer-dependent amplification of nucleic acids (HIP), nicking enzymeamplification reaction (NEAR), or improved multiple displacementamplification (IMDA). In some cases, LAMP amplification can allow for asingle amplification step for Cas12 and Cas13 simultaneously. In someembodiments, LAMP can allow for amplification of target nucleic acidsfor up to three or more than three programmable nucleasessimultaneously. In some embodiments, with RPA, fewer primers are neededand multiplexing can be increased to three or six programmablenucleases. Often, the nucleic acid amplification is performed for nogreater than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 25, 30, 40, 50, or 60 minutes, or any value from 1 to 60minutes. Sometimes, the nucleic acid amplification is performed for from1 to 60, from 5 to 55, from 10 to 50, from 15 to 45, from 20 to 40, orfrom 25 to 35 minutes. Sometimes, the nucleic acid amplification isperformed for from 15 minutes to 60 minutes, from 30 minutes to 60minutes, from 45 minutes to 60 minutes, from 1 minute to 45 minutes,from 15 minutes to 45 minutes, from 30 minutes to 45 minutes, from 1minute to 30 minutes, from 15 minutes to 30 minutes, from 1 minute to 15minutes. Sometimes, the nucleic acid amplification reaction is performedat a temperature of around 20-45° C. In some cases, the nucleic acidamplification reaction is performed at a temperature no greater than 20°C., 25° C., 30° C., 35° C., 37° C., 40° C., 45° C., or any value from20° C. to 45° C. In some cases, the nucleic acid amplification reactionis performed at a temperature of at least 20° C., 25° C., 30° C., 35°C., 37° C., 40° C., or 45° C., or any value from 20° C. to 45° C. Insome cases, the nucleic acid amplification reaction is performed at atemperature of from 20° C. to 45° C., from 25° C. to 40° C., from 30° C.to 40° C., or from 35° C. to 40° C. In some cases, the nucleic acidamplification reaction is performed at a temperature of from 20° C. to45° C., from 25° C. to 45° C., from 30° C. to 45° C., from 35° C. to 45°C., from 40° C. to 45° C., from 20° C. to 37° C., from 25° C. to 37° C.,from 30° C. to 37° C., from 35° C. to 37° C., from 20° C. to 30° C.,from 25° C. to 30° C., from 20° C. to 25° C., or from 22° C. to 25° C.

Kits, methods, or compositions described herein may comprise reagentsfor reverse transcription, amplification, in vitro transcription, or anycombination thereof. In some embodiments, reagents for amplification cancomprise a DNA sequence, dNTPs, a forward primer, a reverse primer, anda polymerase. In some embodiments, reagents for RT-RPA amplification maycomprise a DNA or RNA, RPA primers, deoxynucleotide triphosphates(dNTPs), a polymerase, and a reverse transcriptase enzyme. In someembodiments, reagents for an in vitro transcription (IVT) reaction maycomprise a DNA, NTPs, and an RNA polymerase enzyme (e.g, T7 RNApolymerase). In some embodiments, reagents for an RT-RPA-IVT combinedamplification and transcription reaction may comprise a DNA or RNAsequence, RPA primers, an RPA primer having a T7 promoter, a reversetranscriptase enzyme, dNTPs, NTPs, a recombinase, an RNA polymeraseenzyme (e.g, T7 RNA polymerase), or any combination thereof. In someembodiments, reagents for LAMP amplification may comprise a DNA, aplurality of primers (e.g., four, five, or six primers), dNTPs, and apolymerase. In some embodiments, reagents for RT-LAMP amplification maycomprise an RNA, a plurality of primers (e.g., four, five, or sixprimers), dNTPs, a polymerase, and a reverse transcriptase enzyme. Insome embodiments, reagents for RT-LAMP-IVT may comprise an RNA, aplurality of primers (e.g., four, five, or six primers), a primer havinga T7 promoter, dNTPs, NTPs, a polymerase enzyme, a reverse transcriptaseenzyme, and an RNA polymerase (e.g., T7 RNA polymerase). In someembodiments, reagents for SIBA amplification may comprise a DNA having aprotospacer adjacent motif (PAM), dNTPs, and a polymerase enzyme. Insome embodiments, reagents for RT-SIBA amplification may comprise an RNAhaving a protospacer adjacent motif (PAM), primers, dNTPs, a polymeraseenzyme, and a reverse transcriptase enzyme. The present disclosureprovides devices and methods that allow for rapid reverse transcription,amplification, and/or in vitro transcription of target nucleic acids ofinterest, in one step. Thus, the general reagents for reversetranscription, amplification, and/or in vitro transcription can becombined regardless of the specific method of amplification used.

Sometimes, the total time for the performing the method described hereinis no greater than 3 hours, 2 hours, 1 hour, 50 minutes, 40 minutes, 30minutes, 20 minutes, or any value from 3 hours to 20 minutes. Often, amethod of nucleic acid detection from a raw sample comprises proteasetreating the sample for no more than 15 minutes, amplifying (can also bereferred to as pre-amplifying) the sample for no more than 15 minutes,subjecting the sample to a programmable nuclease-mediated detection, andassaying nuclease mediated detection. The total time for performing thismethod, sometimes, is no greater than 3 hours, 2 hours, 1 hour, 50minutes, 40 minutes, 30 minutes, 20 minutes, or any value from 3 hoursto 20 minutes. The total time for performing this method, sometimes, isfrom 20 minutes to 3 hours, from 30 minutes to 3 hours, from 45 minutesto 3 hours, from 1 hour to 3 hours, from 1.5 hours to 3 hours, from 2hours to 3 hours, from 2.5 hours to 3 hours, from 20 minutes to 2.5hours, from 30 minutes to 2.5 hours, from 45 minutes to 2.5 hours, from1 hour to 2.5 hours, from 1.5 hours to 2.5 hours, from 2 hours to 2.5hours, from 20 minutes to 2 hours, from 30 minutes to 2 hours, from 45minutes to 2 hours, from 1 hour to 2 hours, from 1.5 hours to 2 hours,from 20 minutes to 1.5 hours, from 30 minutes to 1.5 hours, from 45minutes to 1.5 hours, from 1 hour to 1.5 hours, from 20 minutes to 1hour, from 30 minutes to 1 hour, from 45 minutes to 1 hour, from 20minutes to 45 minutes, from 30 minutes to 45 minutes, or from 20 minutesto 30 minutes. Often, the protease treatment is Proteinase K. Often theamplifying is thermal cycling amplification. Sometimes the amplifying isisothermal amplification.

Described herein are collection pad region that provide a region tocollect the sample that flows down the support medium. Often thecollection pads are placed downstream of the detection region andcomprise an absorbent material. The collection pad can increase thetotal volume of sample that enters the support medium by collecting andremoving the sample from other regions of the support medium. Thisincreased volume can be used to wash unbound conjugates away from thedetection region to lower the background and enhance assay sensitivity.When the design of the support medium does not include a collection pad,the volume of sample analyzed in the support medium may be determined bythe bed volume of the support medium. The collection pad may provide areservoir for sample volume and may help to provide capillary force forthe flow of the sample down the support medium.

The collection pad may be prepared from various materials that arehighly absorbent and able to retain fluids. Often the collection padscomprise cellulose filters. In some instances, the collection padscomprise cellulose, cotton, woven meshes, polymer-based matrices. Thedimension of the collection pad, usually the length of the collectionpad, may be adjusted to change the overall volume absorbed by thesupport medium.

The support medium described herein may have a barrier around the edgeof the support medium. Often the barrier is a hydrophobic barrier thatfacilitates the maintenance of the sample within the support medium orflow of the sample within the support medium. Usually, the transportrate of the sample in the hydrophobic barrier is much lower than throughthe regions of the support medium. In some cases, the hydrophobicbarrier is prepared by contacting a hydrophobic material around the edgeof the support medium. Sometimes, the hydrophobic barrier comprises atleast one of wax, polydimethylsiloxane, rubber, or silicone.

Any of the regions on the support medium can be treated with chemicalsto improve the visualization of the detection spot and positive controlspot on the support medium. The regions can be treated to enhanceextraction of nucleic acid in the sample, to control the transport ofthe reacted reagents and sample or the conjugate to other regions of thesupport medium, or to enhance the binding of the cleaved detectionmoiety to the conjugate binding molecule on the surface of the conjugateor to the capture molecule in the detection region. The chemicals maycomprise detergents, surfactants, buffers, salts, viscosity enhancers,or polypeptides. In some instances, the chemical comprises bovine serumalbumin. In some cases, the chemicals or physical agents enhance flow ofthe sample with a more even flow across the width of the region. In somecases, the chemicals or physical agents provide a more even mixing ofthe sample across the width of the region. In some cases, the chemicalsor physical agents control flow rate to be faster or slower in order toimprove performance of the assay. Sometimes, the performance of theassay is measured by at least one of shorter assay time, longer timesduring cleavage activity, longer or shorter binding time with theconjugate, sensitivity, specificity, or accuracy.

Packaging Stability

Disclosed herein are stable compositions of the reagents and theprogrammable nuclease system for use in the methods as discussed above.These stable compositions of the reagents and the programmable nucleaseare, for example, consistent with fluidic devices disclosed herein fordetection of a target nucleic acid within the sample, wherein thefluidic device may comprise multiple pumps, valves, reservoirs, andchambers for sample preparation, amplification of a target nucleic acidwithin the sample, mixing with a programmable nuclease, and detection ofa detectable signal arising from cleavage of detector nucleic acids bythe programmable nuclease. The reagents and programmable nuclease systemdescribed herein may be stable in various storage conditions includingrefrigerated, ambient, and accelerated conditions. Disclosed herein arestable reagents. The stability may be measured for the reagents andprogrammable nuclease system themselves or the reagents and programmablenuclease system present on the support medium.

In some instances, stable as used herein refers to a reagents havingabout 5% w/w or less total impurities at the end of a given storageperiod. Stability may be assessed by HPLC or any other known testingmethod. The stable reagents may have about 10% w/w, about 5% w/w, about4% w/w, about 3% w/w, about 2% w/w, about 1% w/w, or about 0.5% w/wtotal impurities at the end of a given storage period. The stablereagents may have from 0.5% w/w to 10% w/w, from 1% w/w to 10% w/w, from2% w/w to 10% w/w, from 3% w/w to 10% w/w, from 5% w/w to 10% w/w, from7% w/w to 10% w/w, from 8% w/w to 10% w/w, from 0.5% w/w to 8% w/w, from1% w/w to 8% w/w, from 2% w/w to 8% w/w, from 3% w/w to 8% w/w, from 5%w/w to 8% w/w, from 7% w/w to 8% w/w, from 0.5% w/w to 7% w/w, from 1%w/w to 7% w/w, from 2% w/w to 7% w/w, from 3% w/w to 7% w/w, from 5% w/wto 7% w/w, from 0.5% w/w to 5% w/w, from 1% w/w to 5% w/w, from 2% w/wto 5% w/w, from 3% w/w to 5% w/w, from 0.5% w/w to 3% w/w, from 1% w/wto 3% w/w, from 2% w/w to 3% w/w, from 0.5% w/w to 2% w/w, from 1% w/wto 2% w/w, or from 0.5% w/w to 1% w/w total impurities at the end of agiven storage period.

In some embodiments, stable as used herein refers to a reagents andprogrammable nuclease system having about 10% or less loss of detectionactivity at the end of a given storage period and at a given storagecondition. Detection activity can be assessed by known positive sampleusing a known method. Alternatively or combination, detection activitycan be assessed by the sensitivity, accuracy, or specificity. In someembodiments, the stable reagents has about 10%, about 9%, about 8%,about 7%, about 6%, about 5%, about 4%, about 3%, about 2%, about 1%, orabout 0.5% loss of detection activity at the end of a given storageperiod. In some embodiments, the stable reagents have from 0.5% to 10%,from 1% to 10%, from 2% to 10%, from 3% to 10%, from 5% to 10%, from 7%to 10%, from 8% to 10%, from 0.5% to 8%, from 1% to 8%, from 2% to 8%,from 3% to 8%, from 5% to 8%, from 7% to 8%, from 0.5% to 7%, from 1% to7%, from 2% to 7%, from 3% to 7%, from 5% to 7%, from 0.5% to 5%, from1% to 5%, from 2% to 5%, from 3% to 5%, from 0.5% to 3%, from 1% to 3%,from 2% to 3%, from 0.5% to 2%, from 1% to 2%, or from 0.5% to 1% lossof detection activity at the end of a given storage period.

In some embodiments, the stable composition has zero loss of detectionactivity at the end of a given storage period and at a given storagecondition. The given storage condition may comprise humidity of equal toor less than 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%relative humidity. The controlled storage environment may comprisehumidity from 0% to 50% relative humidity, from 0% to 40% relativehumidity, from 0% to 30% relative humidity, from 0% to 20% relativehumidity, or from 0% to 10% relative humidity. The controlled storageenvironment may comprise humidity from 0% to 100%, from 10% to 100%,from 20% to 100%, from 30% to 100%, from 50% to 100%, from 70% to 100%,from 80% to 100%, from 90% to 100%, from 0% to 90%, from 10% to 90%,from 20% to 90%, from 30% to 90%, from 50% to 90%, from 70% to 90%, from80% to 90%, from 0% to 80%, from 10% to 80%, from 20% to 80%, from 30%to 80%, from 50% to 80%, from 70% to 80%, from 0% to 70%, from 10% to70%, from 20% to 70%, from 30% to 70%, from 50% to 70%, from 0% to 50%,from 10% to 50%, from 20% to 50%, from 30% to 50%, from 0% to 30%, from10% to 30%, from 20% to 30%, from 0% to 20%, from 10% to 20%, from 0% to10%, or from 20% to 40%, relative humidity. The controlled storageenvironment may comprise temperatures of about −100° C., about −80° C.,about −20° C., about 4° C., about 25° C. (room temperature), or about40° C. The controlled storage environment may comprise temperatures from−80° C. to 25° C., or from −100° C. to 40° C. The controlled storageenvironment may comprise temperatures from −20° C. to 40° C., from −20°C. to 4° C., or from 4° C. to 40° C. The controlled storage environmentmay protect the system or kit from light or from mechanical damage. Thecontrolled storage environment may be sterile or aseptic or maintain thesterility of the light conduit. The controlled storage environment maybe aseptic or sterile.

The kit or system can be packaged to be stored for extended periods oftime prior to use. The kit or system may be packaged to avoiddegradation of the kit or system. The packaging may include desiccantsor other agents to control the humidity within the packaging. Thepackaging may protect the kit or system from mechanical damage orthermal damage. The packaging may protect the kit or system fromcontamination of the reagents and programmable nuclease system. The kitor system may be transported under conditions similar to the storageconditions that result in high stability of the reagent or little lossof reagent activity. The packaging may be configured to provide andmaintain sterility of the kit or system. The kit or system can becompatible with standard manufacturing and shipping operations.

Definitions

Unless otherwise defined, all technical terms used herein have the samemeaning as commonly understood by one of ordinary skill in the art towhich this invention belongs. As used in this specification and theappended claims, the singular forms “a,” “an,” and “the” include pluralreferences unless the context clearly dictates otherwise. Any referenceto “or” herein is intended to encompass “and/or” unless otherwisestated.

As used herein, the term “comprising” and its grammatical equivalentsspecifies the presence of stated features, integers, steps, operations,elements, and/or components, but do not preclude the presence oraddition of one or more other features, integers, steps, operations,elements, components, and/or groups thereof. As used herein, the term“and/or” includes any and all combinations of one or more of theassociated listed items.

Unless specifically stated or obvious from context, as used herein, theterm “about” in reference to a number or range of numbers is understoodto mean the stated number and numbers +/−10% thereof, or 10% below thelower listed limit and 10% above the higher listed limit for the valueslisted for a range.

As used herein the terms “individual,” “subject,” and “patient” are usedinterchangeably and include any member of the animal kingdom, includinghumans.

As used herein the term “antibody” refers to, but not limited to, amonoclonal antibody, a synthetic antibody, a polyclonal antibody, amultispecific antibody (including a bi-specific antibody), a humanantibody, a humanized antibody, a chimeric antibody, a single-chain Fv(scFv) (including bi-specific scFvs), a single chain antibody, a Fabfragment, a F(ab′) fragment, a F(ab′)2 fragment, a disulfide-linked Fvs(sdFv), or an epitope-binding fragment thereof. In some cases, theantibody is an immunoglobulin molecule Or an immunologically activeportion of an immunoglobulin molecule. In some instances, an antibody isanimal in origin including birds and mammals. Alternately, an antibodyis human or a humanized monoclonal antibody.

FIG. 1 shows a bar graph with relative fluorescence on the y-axisranging from 0 to 1 in increments of 0.2. On the y-axis are differentgroups including FAM-UU, FAM-UU-long, FAM-AU, FAM-UG, FAM-U10, FAM-U5,FAM-U8, and RNAseAlert. Within each group, from left to right, the barsshow no enzyme, +RNAse, Cas13a; no target, and Cas13a +target.

FIG. 2 shows a plot of crRNA along the horizontal edge and activatorsalong the vertical edge. crRNA include, from left to right, chlamydia,E. coli, and E. coli+chlamydia mixed. Activators include, from bottom totop, include both, chalmydia, E. coli only, and none. The strength ofthe shading indicates the fluorescence (AU). At right is a scale barshowing lighter shades indicate a lower fluorescence intensity anddarker shades indicate a higher fluorescence.

FIG. 3 shows a graph of crRNA on the x-axis and fluorescence (AU) on they-axis from 0 to 8000 in increments of 2000. crRNA groups include crRNAs1+2+3, crRNA 1, crRNA 2, and crRNA 3. Within each group is a pair ofbars. From left to right the bars are 0.0 nM target RNA and 0.001 nMtarget RNA.

FIG. 4 shows a graph of fluorophore on the x-axis and raw fluorescence(AU) on the y-axis from 0 to 5000 in increments of 1000. Thefluorophores shown include FAM, AlexaFluor 594, ATTO 633, TYE 665, andIRDYE 700.

FIG. 5A shows three graphs, which from left to right are titled RNAseinhibitor non, RNAse inhibitor RiboLock, and RNAse inhibitor PVS. Thex-axis of each graph shows two groups of urine fraction including “0”and “0.18”. Shown on the y-axis of each graph is fluorescence (AU) from0 to 3000 in increments of 500, Within each urine fraction group are apair of bars, which from left to right are 0.0 nM target RNA and 0.09 nMtarget RNA.

FIG. 5B shows a graph titled RNAse inhibitor None. The x-axis of thegraph shows two groups of urine fraction including “0” and “0.18”. Shownon the y-axis of each graph is fluorescence (AU) from 0 to 12000 inincrements of 2000. Within each urine fraction group are a pair of bars,which from left to right are 0.0 nM target RNA and 0.09 nM target RNA.

FIG. 6 shows a graph titled performance of fluorophores in urine. Thex-axis of the graph shows fluorophores including, from left to right,FAM, AlexaFluor 594, ATTO 633, TYE 665, and IRDYE 700. On the y-axis isnormalized fluorescence (FAM) from 0 to 1.5 in increments of 0.5.

FIG. 7A shows a graph entitled “Reporter performance in detection assay100 fM target RNA”. Shown on the x-axis are three groups includingFAM-U5, TYE665-U5, and IRDYE700-U5. Shown on the y-axis is backgroundsubtracted fluorescence (AU) from 0 to 8000 in increments of 2000.Within each group is a pair of bars, which from left to right, areoriginal buffer and MBuffer1.

FIG. 7B shows a graph entitled “Reporter performance in detection assayin urine 10 pM target RNA”. Shown on the x-axis are three groupsincluding FAM-U5, TYE665-U5, and IRDYE700-U5. Shown on the y-axis isbackground subtracted fluorescence (AU) from 0 to 50000 in increments of10000. Within each group is a pair of bars, which from left to right,are original buffer and MBuffer1.

FIG. 8A shows a schematic of guide RNA (gRNA) above, and binding to, aspecies-specific locus of P. falciparum, a gRNA above, and binding to, aWT allele of kelch13, and a gRNA above, and binding to, a C580Y alleleof kelch13. The gRNA for detection of a WT allele of kelch13 binds tothe WT allele of kelch13, but does not bind to the kelch13 C580Y allele.The gRNA for detection of the kelch13 C580Y allele binds to the kelch13C580Y allele, but does not bind to the kelch13 WT allele.

FIG. 8B shows a graph entitled “Cas12a discrimination between WT andsingle-nucleotide mutation. The x-axis shows guide RNA/target pairgroups and the y-axis shows background subtracted fluorescence from 0 to15000 in increments of 5000. The guide RNA/target pair groups include WTgRNA WT target, WT gRNA mut target, mut gRNA WT target, and mut gRNA muttarget.

FIG. 8C at left shows a schematic, which from top to bottom shows aCas13/gRNA complex (which functions for species detection) and aCas12/gRNA complex (which functions for SNP discrimination) being addedto an eppendorph. The Cas13/gRNA complex bound to the 16S region of thetarget gene and the Cas12/gRNA complex is shown bound to the 23s (WT) or23S (mutant) region of the target gene (depending on the composition ofthe gRNA). Cas12/gRNA complexes specific to the mutant do not bind thewild type and Cas12/gRNA complexes specific to the wild type do not bindthe mutant. At the right are grid plots of N. gonorrhoeae infection. Atthe top right is a grid plot, titled antibiotic susceptible, with Cas13(16S) in the left column, Cas12 (23S-SNP) in the right column, WT in thetop row, and mutant in the bottom row. Cas12 crRNA was used. The darkera quadrant, the higher the fluorescence, as indicated in the scale barat the very bottom right of the image. The scale bar shows fluorescencefrom 0 to 7500 in increments of 1500. At the bottom right is a gridplot, titled antibiotic resistant, with Cas13 (16S) in the left column,Cas12 (23S-SNP) in the right column, WT in the top row, and mutant inthe bottom row. Cas12 crRNAwas used. The darker a quadrant, the higherthe fluorescence, as indicated in the scale bar at the very bottom rightof the image.

FIG. 9 shows a schematic, which from left to right shows, Steps 1 to 4of a workflow. Under Step 1 is “sample preparation” in an oval. UnderStep 2 is “nucleic acid amplification” in an oval. Under Step 3 is“programmable nuclease reaction incubation” in a rectangle. Under Step 4is “detection (readout)” in a rectangle.

FIG. 10 depicts at right a filtration device shaped like a syringe. Atleft are three samples, which from top to bottom are cheek/facial swab,urine specimen collector, and fingerprint.

FIG. 11 shows at top a schematic entitled “device 2.1-essentialselements only/no amplification”. A sample is depicted entering throughP1, which is connected vertically below to V1. V1 is adjacent to V2,which is connected vertically above to P2 through which pre-complexedprogrammable nuclease mix is introduced. To the right of V1 is a twistedregion labeled S1. To the right of S1 is an incubation and detectionchamber, labeled C1. To the right of C1 is V3, which is connectedvertically above to P3, which is the collection outlet. Shown in themiddle of the schematic is a fluidic device entitled “device2.2-one-chamber reaction with amplification. A sample is depictedentering through P1, which is connected vertically below to V1. V1 isadjacent to V2, which is connected vertically above to P2 through whichamplification mix is introduced. V2 is adjacent to V2, which connectedvertically above to P3 through which pre-complexed programmable nucleasemix is introduced. To right of V3 is a twisted region labeled S1. To theright of S1 is an incubation and detection chamber, labeled C1. To theright of C1 is V4, which is connected vertically above to P4, which isthe collection outlet. Shown at bottom is another fluidic deviceentitled “device 2.3-two-chamber reaction with amplification”. A sampleis depicted entering through P1, which is connected vertically below toV1. V1 is adjacent to V2, which is connected vertically above to P2through which amplification mix is introduced. To the right of V2 is atwisted region labeled S1. To the right of S1 is an incubation chamberlabeled C1. To the right of C1 is V3, which is connected verticallyabove to P3, through which pre-complexed programmable nuclease mix isintroduced. To the right of V3 is another serpentine region labeled S2.To the right of S2 is an incubation and detection chamber labeled C2. Tothe right of C2 is V4, which is connected vertically above to P4, whichis the collection outlet.

FIG. 12 shows at top is “(a) fluorescence readout” and depicts arectangular chip substrate surface with a thin film planar heater shownas a colored in rectangular region. Above the chip is a drawing of afluorescence excitation/detection apparatus. Shown below is a “(b)electrochemical readout”. The electrochemical readout shows twoschematics. The top schematic is titled “solid-phase detection usingstreptavidin signal amplification”. At left is a rectangular surfacedepicting the top chamber surface coated with ssDNA labeled with biotin,which is shown as stars. Directly below is an electrode surface withstreptavidin, which is shown as hexagons. Shown to the right of thefunctionalized chambers is a graph of voltage on the x-axis versuscurrent on the y-axis, where the graph is titled “LOW”. To the right isan arrow showing introduction of a programmable nuclease, which isdepicted as a pair of scissors, and which is shown to cleave the biotinoff the top surface. The biotin is depicted as attached to thestreptavidin. Shown further to the right is a graph of voltage on thex-axis versus current on the y-axis, where the graph is titled “HIGH”.Shown below is the second schematic titled “solid-phase detection usingimmobilized electroactive oligos”. Shown at the left of the schematic isa rectangular electrode surface with ssNA/Fc-NTP. The surface isfunctionalize with electroactive moieties depicted as tree-likestructures with ferrocene shown in circles. To the right is a graph ofvoltage on the x-axis versus current on the y-axis and where the graphis titled “HIGH”. Further to the right is an arrow showing introductionof a programmable nuclease, which is depicted as a pair of scissors, andwhich is shown to cleave the Fc circles. Further to the right is a graphof voltage on the x-axis versus current on the y-axis and where thegraph is titled “LOW”.

FIG. 13 shows a sample being introduced at P1, which is connectedvertically below to V1. V1 is adjacent to V2, which is connectedvertically above to isothermal amplification mix. To the right of V2 isa serpentine channel labeled S1. Further to the right is an incubationchamber labeled C1. To the right of C1 is V3, which is connectedvertically above to P3, through which pre-complexed programmablenuclease mix is introduced. To the right of V3 is another serpentinechannel labeled S2 and further to the right is another incubationchamber labeled C2. To the right of C2 is V4, which is connectedvertically above to P4 through which sucrose or a colorimetric reagentis introduced. To the right of V4 is another serpentine channel labeledS3 and further to the right is a detection chamber labeled C3 To theright of C3 is V5, which is connected vertically above to P5. Below isan exploded view diagram of the C2 incubation chamber. The schematic isof a top chamber depicted as a rectangle with a label reading “topchamber surface coated with ssNA conjugated to invertase. Invertase isshown in rectangular boxes labeled “Inv”. Below the top chamber is astructure showing a bottom chamber surface with a thin-film planarheater. Further to the right is an arrow showing introduction of aprogrammable nuclease, which is depicted as a pair of scissors, andwhich is shown to cleave the Invertase. Further below is an explodedview diagram of the detection chamber labeled C3. This exploded viewdiagram shows at top a schematic labeled “(a) optical readout using DNS,or other compound”. At top is “(a) optical readout using DNS, or othercompound” and depicts a rectangular chip substrate surface with a thinfilm planar heater shown as a colored in rectangular region. Above thechip is a camera, or optical sensor. At bottom is “(b) electrochemicalreadout (electrochemical analyzer or glucometer”, which from left toright shows an electrode surface with immobilized glucose oxidase, whichis depicted as a rectangle with an oval labeled “GOx”. Above thefunctionalized electrode surface is a flow diagram which from left toright shows sucrose, an arrow to the right with “Inv” directly above it,and fructose+glucose at the right. To the right of the functionalizedelectrode surface is a graph of voltage on the x-axis versus current onthe y-axis, below which is an electronic reader indicating “LOW”.Further to the right is glucose interacting with the GOx functioanlizedelectrode surface resoluting in H2)2+F-glucono-δ-lactone. To the rightis a graph of voltage on the x-axis versus current on the y-axis, belowwhich is an electronic reader indicating “HIGH”. Below is a key showingthat an invertase-labeled oligo is depicted as a line with a rectanglelabeled “Inv”. Programmable nuclease is depicted as a pair of scissors.The molecular structure of DNS is shown. Glucose oxidase is an ovallabeled as GOx.

FIG. 14B depicts a bar graph of the detection of prostate cancer RNAbiomarkers. The graph shows three sets of three bars, the three setscorresponding to, from left to right, RNA #1, RNA #2, and RNA #3, asdenoted by the x-axis. The y-axis shows background subtractedfluorescence (AU) from 0 to 140,000 in increments of 20,000. The threebars in each set correspond to, from left to right, prostate cancer cellline, cervical cancer cell line, and water. In each set the barcorresponding to the prostate cancer cell line is the highest. In allthree sets, the bar corresponding to water is not visible. The barcorresponding to the cervical cancer cell line is not visible in the RNA#2 set.

FIG. 20A shows a line graph depicting the current as a function ofpotential. Potential (V) is shown on the x-axis from −0.4 to 0.4 inincrements of 0.1. Current (μA) is shown on the y-axis from −20 to 20 inunits of 5. The graph depicts two sets of two lines. Each set of twolines includes one line corresponding to Reporter Only (darker line) andthe other corresponding to Cleaved Reporter (lighter line). In the upperleft corner of the graph, the Reporter Only line is higher than theCleaved Reporter line at lower potential, and the Cleaved Reporter lineis higher than the Reporter Only line at higher potential. In the lowerright corner of the graph, the Cleaved Reporter line is higher than theReporter Only line for all potential values except for from about −0.1to about −0.04.

FIG. 20B shows a line graph depicting the current as a function ofpotential. Potential (V) is shown on the x-axis from −0.4 to 0.1 inincrements of 0.1. Current (μA) is shown on the y-axis from 30 to 55 inunits of 5. The graph depicts two lines corresponding to Reporter Only(darker line) and Cleaved Reporter (lighter line). The Cleaved Reporterline is higher than the Reporter only line at all potential values.

FIG. 27 shows two line graphs corresponding to Cas12 performance after30 min at 52.5C on the left and Cas12 performance after 30 min at 55C onthe right. Each plot depicts four sets of four lines, the first setcorresponding to 1× MBffer3, 1×NE Buffer 4+TWEEN (polysorbate),0.5×IsoAmp, all at a concentration of 1 (solid lines), and the secondset corresponding to 1× MBffer3, 1×NE Buffer 4+TWEEN, 0.5×NE Buffer4+TWEEN, 0.5×IsoAmp, all at a concentration of 0 (dashed lines). In theleft plot, the x-axis show time in minutes from 0 to 60 in increments of20, and the y-axis shows raw fluorescence (AU) from 1,000,000 to7,000,000 in increments of 1,000,000. From 0 to about 30 minutes (30minutes denoted by a vertical dashed line), all lines are substantiallyoverlapping below 1,000,000 AU. After 30 minutes, the linescorresponding to 1× MBffer3, 1×NE Buffer 4+TWEEN, 0.5×NE Buffer 4+TWEEN,all at a concentration of 1, rise rapidly above baseline. The linecorresponding to 0.5×NE Buffer 4+TWEEN at a concentration of 1 is thehighest, followed by 1× MBffer3 at a concentration of 1, the by 1×NEBuffer 4+TWEEN at a concentration of 1. In the right plot, the x-axisshow time in minutes from 0 to 60 in increments of 20, and the y-axisshows raw fluorescence (AU) from 1,000,000 to 6,000,000 in increments of1,000,000. From 0 to about 30 minutes (30 minutes denoted by a verticaldashed line), all lines are substantially overlapping below 1,000,000AU. After 30 minutes, the lines corresponding to 1× MBffer3, 1×NE Buffer4+Tween, 0.5×NE Buffer 4+Tween, all at a concentration of 1, riserapidly above baseline. The line corresponding to 0.5×NE Buffer 4+TWEENat a concentration of 1 is the highest, followed by 1× MBffer3 at aconcentration of 1, the by 1×NE Buffer 4+TWEEN at a concentration of 1.

FIG. 30 depicts a line graph of raw fluorescence over time. The x-axisshows time in minutes from 0.0 to 20.0 in increments of 2.5. The y-axisshows raw fluorescence from 0 to 3, 500,000 in increments of 500,000.The lines depict targets corresponding to Low pH, RT-pool, Low pH+heat,GenMark pool, Deoxycholate, Deoxycholate+heat, CHAPS, CHAPS+heat,Deoxycholate+Urea, Deoxycholate+Urea+heat, Nucleospin gold std, TRITONX-100 (octyl phenol ethoxylate), 10e4, and NTC. The cRNA is IAV. Thehighest lines on the graph correspond to RT-pool, Low pH, and GenMarkpool. The remaining lines, in order from upper left to lower right,correspond to NucleoSpin gold std, Doxycholate and CHAPS+Urea(approximately equal), Low pH+heat, CHAPS+heat, CHAPS+Urea+heat, TRITONX-100, Deoxycholate+Urea, 10e4, and Deoxycholate+Urea+heat. NTC is aflat line at about 1, 500,000.

FIG. 31 depicts a line graph of raw fluorescence over time. The x-axisshows time in minutes from 0.0 to 20.0 in increments of 2.5. The y-axisshows raw fluorescence from 1,000,000 to 3,000,000 in increments of1,000,000. The lines depict targets corresponding to Low pH 0 min, LowpH 3 min, Low pH 5 min, Low pH 10 min, Low pH 15 min, Low pH No EtOH,Low pH+heat 50, Low pH+heat 100, Untreated, RT-pool, 10e5, 10ebb 4,10e3, and NTC. The crRNA is IAV. The two highest lines correspond to LowpH 0 min and RT-pool. The remaining lines, from upper left to lowerright, correspond to Low pH 5 min, Low pH No EtOH, Low pH 15 min, Low pH10 min, 10e5, Low pH+heat 100, Low pH+heat 50, Untreated, 10e4, 10e3,and NTC.

FIG. 36 depicts a flow chart and two line graphs. The flow chart showsfour boxes. The top box reads “DNA/RNA.” The remaining three boxes read,from top to bottom, “RPA/RT-RPA,” “In vitro transcription,” and “Cas13aDetection.” Both plots show raw fluorescence over time. The x-axis showsminutes from 0 to 40 in increments of 10. The y-axis shows rawfluorescence (AU) from 0 to 60,000 in increments of 20,000. Both plotsshow two sets of two lines corresponding to on-target and off-targeteach at 500 aM (solid lines), and on-target and off-target each at 0 aM(dashed lines). The left plot depicts PPRV. In the left plot, the linecorresponding to on-target at 500 aM rises over time. The remaininglines appear approximately flat. The right plot shows PPRV-noIVT. Allfour lines are approximately flat.

FIG. 38 depicts a flow chart and four line graphs. The flow chart showsfour boxes. The top box reads “DNA/RNA.” The remaining three boxes read,from top to bottom, “RPA/RT-RPA,” “In vitro transcription,” and “Cas13aDetection.” All four plots show raw fluorescence over time. The x-axisof all four plots shows minutes from 0 to 20 in increments of 10. They-axis of all four plots shows raw fluorescence (AU) from 0 to 25,000 inincrements of 5,000. All four plots show two lines corresponding tocrRNA on-target and off-target. The upper left plot shows +RT and +UMT.The on-target line rises over time, and the off-target line appearsapproximately flat. The lower left plot shows +RT and −UMT. Theon-target line rises over time, and the off-target line appearsapproximately flat. The upper right plot shows −RT and +UMT. Both linesappear approximately flat. The lower right plot shows −RT and −UMT. Bothlines appear approximately flat, but the on-target line is above theoff-target line.

FIG. 41B shows a bar graph depicting time to result (lower is better).The graph shows six sets of four bars each. The six sets of barscorrespond to temperatures (C) of, from left to right, of 74, 72, 70,68, 66, and 64, as shown on the x-axis. The four bars in each set show,from left to right, Hela-total-RNA, Mouse-liver-RNA, Hela-DNA, and NTC.The y-axis shows time to result (minutes) from 0 to 40 in increments of5. At all six temperatures, the bars corresponding to Mouse-liver-RNAand NTC have a time to result of 40 or more. At all six temperatures,Hela-total-RNA is the next highest, and Hela-DNA is the lowest.

FIG. 41C depicts three line graphs corresponding to, from left to right,crRNA=off-target, crRNA=on-target #1, and crRNA=on-target #2. For allthree plots, the x-axis shows minutes from 0 to 75 in increments of 25,and the y-axis shows raw fluorescence (AU) from 0 to 1, 500,000 inincrements of 500,000. Each plot depicts three lines corresponding toTargets, the lines representing Hela-RNA, Hela-DNA, Mouse-liver RNA, andNTC. On the left plot and the right plot, all four lines areapproximately flat. In the middle plot, the lines corresponding toHela-DNA and Hela-RNA rise over time, with Hela-DNA being the highest.Mouse-liver-RNA and NTC are the lowest.

FIG. 42 depicts a flow chart and six line graphs. The flow chart showsthree boxes labeled, from top to bottom, “DNA/RNA,” “LAMP/RT-LAMP,” and“Cas12a Detection.” The six line graphs show fluorescence over time. Inall six plots, the x-axis shows minutes from 0 to 75 in increments of25, and the y-axis shows raw fluorescence (AU) from 0 to 60,000 inincrements of 20,000. All six plots show three lines corresponding todifferent crRNAs. The three lines show on-target #1, on-target #2, andoff-target. The upper left plot shows Primers=IAV1, Target=IAV. The linecorresponding to on-target #2 rises over time and is the highest. Theline corresponding to off-target rises slightly over time. The linecorresponding to on-target #1 appear approximately flat. The uppermiddle plot shows Primers=IAV2, Target=IAV. The line corresponding toon-target #2 rises over time and is the highest. The line correspondingto on-target #1 rises over time, but is not as high as on-target #2. Theline corresponding to off-target rises slightly over time and is thelowest. The upper right plot shows Primers=IAV3, Target=IAV. The linecorresponding to on-target #1 rises over time and is the highest. Theline corresponding to off-target rises slightly over time, but is not ashigh as on-target #1. The line corresponding to on-target #2 appear lowon the graphs and appear approximately flat. The lower left plot showsPrimers=IAV1, Target=NTC. The line corresponding to on-target #2 risesover time and is the highest. The line corresponding to off-target risesslightly over time, but is not as high as on-target #2. The linecorresponding to on-target #1 appears approximately flat. The lowermiddle plot shows Primers=IAV2, Target=NTC. The line corresponding tooff target rises slightly over time. The lines corresponding toon-target #1 and on-target #2 appear approximately flat. The lower rightplot shows Primers=IAV3, Target=NTC. The line corresponding to offtarget rises slightly over time. The lines corresponding to on-target #1and on-target #2 appear low on the graphs and look approximately flat.

FIG. 43 depicts a flow chart and three line graphs. The flow chart showsthree boxes labeled, from top to bottom, “DNA/RNA,” “LAMP/RT-LAMP,” and“Cas12a Detection.” The three line graphs show fluorescence over time.In all three plots, the x-axis shows minutes from 0 to 75 in incrementsof 25, and the y-axis shows raw fluorescence (AU) from 0 to 60,000 inincrements of 20,000. All three plots show three lines corresponding todifferent crRNAs. The three lines IBV #1, IBV #2, and IBV #3. The leftplot shows Target=IAV. All three lines appear approximately flat. Themiddle plot shows Target=IBV. The line corresponding to IBV #3 risesover time and is the highest. The line corresponding to IBV #2 risesover time, but not as rapidly as IBV #3. The line corresponding to IBV#1 appears approximately flat. The right plot shows Target=NTC. Allthree lines appear approximately flat.

FIG. 45B shows six line graphs. In all six plots, the x-axis showsminutes from 0 to 75 in increments of 25, and the y-axis shows rawfluorescence (AU) from 0 to 60,000 in increments of 20,000. All sixplots show two lines corresponding to concentrations of 10000 and 0. Theupper left plot shows Target=IAV, crRNA=IAV. The line corresponding to10000 rises over time and is the highest. The line corresponding to 0appear approximately flat. The upper middle plot shows Target=IBV,crRNA=IAV. Neither line is visible. The upper right plot showsTarget=IAV and IBV, crRNA=IAV. The line corresponding to 10000 risesover time and is the highest. The line corresponding to 0 appearsapproximately flat. The lower left plot shows Target=IAV, crRNA=IBV.Neither line is visible. The lower middle plot shows Target=IBV,crRNA=IBV. The line corresponding to 10000 rises over time and is thehighest. The line corresponding to 0 appear approximately flat. Thelower right plot shows Target=IAV and IBV, crRNA=IBV. The linecorresponding to 10000 rises over time and is the highest. The linecorresponding to 0 appears approximately flat.

FIG. 46 depicts a flow chart and four line graphs. The flow chart hasfive boxes. The top box reads “viral RNA,” the middle box reads“multiplexed RN-LAMP,” and the remaining boxes read, from left to right,“Cas12 Influenza A detection,” “Cas12 Influenza B detection,” and“Cas12a internal amp. detection.” The four plots depict fluorescenceover time. The x-axis of all four plots shows minutes from 0 to 80 inincrements of 20, and the y-axis shows raw fluorescence (AU) from 0 to50,000 in increments of 10,000. Each plot shows three linescorresponding to different crRNAs, IAV, IBV, and Mammoth IAC. Theleft-most plot depicts IAV. The line corresponding to IAV rises overtime. The second plot from the left shows IBV. The line corresponding toIBV rises over time. The second plot from the right depicts IAV and IBV.The line corresponding to IBV rises over time and is the highest. Theline corresponding to IAV rises over time, but is not as high as IBV.The right-most plot depicts IAV, IBV, and Mammoth IAC. The linecorresponding to IBV rises over time and is the highest. The linecorresponding to Mammoth IAC rises over time, but is not as high as IBV.The line corresponding to IAV appears approximately flat.

FIG. 50 shows two line plots. Both plots show fluorescence over time.The x-axis of both plots shows time (minutes) from 0 to 80 in incrementsof 20, and the y-axis shows raw fluorescence (AU) from 0 to 3500 inincrements of 500. Each plot depicts eight lines corresponding to eightdifferent tRNA concentrations (nm/μL) of 400, 300, 200, 100, 40, 20, 10and 0, from darkest line to lightest line. The left plot depicts 0.001nM activator (signal). All eight lines rise over time. The lines, fromupper left to lower right, correspond to 10, 20, 0, 40, 100, 200, 300,and 400. The right plot depicts 0 nM activator (background). The linescorresponding to 0, 10, and 20 rise slightly over time, with 0 being thehighest, followed by 10, and 20 being the lower of the three. The linescorresponding to 40, 100, 200, 300, and 400 appear approximately flat.

FIG. 51A shows two line plots. Both plots show fluorescence over time.The x-axis of both plots shows time (minutes) from 0 to 80 in incrementsof 20, and the y-axis shows raw fluorescence (AU) from 0 to 3500 inincrements of 500. Each plot depicts eight lines corresponding to eightdifferent Urea concentrations (mM) of 1400, 800, 600, 400, 300, 200, 50,from darkest line to lightest line, and 0. The left plot depicts 0.001nM activator (signal). The lines corresponding 1400 and 800 appearapproximately flat. The remaining lines rise slightly over time. Inorder of highest to lowest, the remaining lines correspond to 50, 0,200, 300, 400, and 600. The right plot depicts 0 nM activator(background). All eight lines appear approximately flat.

FIG. 51B shows two line plots. Both plots show fluorescence over time.The x-axis of both plots shows time (minutes) from 0 to 80 in incrementsof 20, and the y-axis shows raw fluorescence (AU) from 0 to 3500 inincrements of 500. Each plot depicts eight lines corresponding to eightdifferent SDS concentrations (%) of 2.0, 1.2, 1.0, 0.8, 0.5, 0.2, 0.1,from darkest line to lightest line, and 0.0. The left plot depicts 0.001nM activator (signal). The line corresponding to 0.0 rises over time.The lines corresponding to 2.0, 1.2, 1.0, 0.8, 0.5, 0.2, and 0.1 appearapproximately flat. The right plot depicts 0 nM activator (background).All eight lines appear approximately flat.

FIG. 52A shows a bar graph depicting florescence at different saltconcentrations. The x-axis shows NaCl, and the y-axis shows backgroundsubtracted fluorescence (AU) from 0 to 14,000 in increments of 2,000.The eight bars, from left to right, show salt conc (mM) of 0, 10, 20,50, 60, 70, 80, and 120.

FIG. 52B shows a bar graph depicting florescence at different saltconcentrations. The x-axis shows KCl, and the y-axis shows backgroundsubtracted fluorescence (AU) from 0 to 14,000 in increments of 2,000.The eight bars, from left to right, show salt conc (mM) of 0, 10, 20,50, 60, 70, 80, and 120.

FIG. 53A shows a bar graph depicting florescence at different DTTconcentrations. The x-axis shows NaCl-DTT, and the y-axis showsbackground subtracted fluorescence (AU) from 0 to 16,000 in incrementsof 2,000. The seven bars, from left to right, show DTT conc (mM) of 0,0.1, 1.0, 2.0, 3.0, 4.0, and 10.0.

FIG. 53B shows a bar graph depicting florescence at different DTTconcentrations. The x-axis shows KCl-DTT, and the y-axis showsbackground subtracted fluorescence (AU) from 0 to 16,000 in incrementsof 2,000. The seven bars, from left to right, show DTT conc (mM) of 0,0.1, 1.0, 2.0, 3.0, 4.0, and 10.0.

FIG. 54 shows 16 line plots. All 16 μlots show fluorescence over time.The x-axis of all 16 μlots shows minutes from 0 to 75 in increments of25, and the y-axis shows raw fluorescence (AU) from 0 to 50,000 inincrements of 10,000. Each plot shows two lines corresponding toactivator concentrations of 1 pM or 0 pM. The plots in the top row showdifferent reporters with Buffer=RNAlessPB. The arrangement of the linesin each plot in the top row, from left to right, are as follows: In theplot showing Reporter=U5, the line corresponding to 1 pM rises overtime, and the line corresponding to 0 pM appears approximately flat. Inthe plot showing Reporter=UU, the line corresponding to 1 pM rises overtime, and the line corresponding to 0 pM appears approximately flat. Inthe plot showing Reporter=UG, the line corresponding to 1 pM rises overtime, and the line corresponding to 0 pM rises over time andsubstantially overlaps the line corresponding to 1 pM. In the plotshowing Reporter=AU, the line corresponding to 1 pM rises over time, andthe line corresponding to 0 pM rises over time but remains lower thanthe line corresponding to 1 pM. In the plot showing Reporter=UUlong, theline corresponding to 1 pM rises slightly over time, and the linecorresponding to 0 pM appears approximately flat. In the plot showingReporter=U8, the line corresponding to 1 pM rises over time, and theline corresponding to 0 pM rises slightly over time but remains lowerthan the line corresponding to 1 pM. In the plot showing Reporter=U10,the line corresponding to 1 pM rises over time, and the linecorresponding to 0 pM rises over time but remains lower than the linecorresponding to 1 pM. In the plot showing Reporter=TYE665U5, the linecorresponding to 1 pM rises over time, and the line corresponding to 0pM appears approximately flat. The plots in the bottom row showdifferent reporters with Buffer=regularPB. The arrangement of the linesin each plot in the bottom row, from left to right, are as follows: Inthe plot showing Reporter=U5, the line corresponding to 1 pM rises overtime, and the line corresponding to 0 pM appears approximately flat. Inthe plot showing Reporter=UU, the line corresponding to 1 pM rises overtime, and the line corresponding to 0 pM appears approximately flat. Inthe plot showing Reporter=UG, both lines appear approximately flat. Inthe plot showing Reporter=AU, the line corresponding to 1 pM risesslightly over time, and the line corresponding to 0 pM appearsapproximately flat. In the plot showing Reporter=UUlong, the linecorresponding to 1 pM rises slightly over time, and the linecorresponding to 0 pM appears approximately flat. In the plot showingReporter=U8, the line corresponding to 1 pM rises over time, and theline corresponding to 0 pM appears approximately flat. In the plotshowing Reporter=U10, the line corresponding to 1 pM rises over time,and the line corresponding to 0 pM appears approximately flat. In theplot showing Reporter=TYE665U5, the line corresponding to 1 pM risesover time, and the line corresponding to 0 pM appears approximatelyflat.

FIG. 55 shows a bar graph of buffer optimization—take 3, 60 minutes,0.001 nM activator. The y-axis shows background subtracted fluorescence(AU) from 0 to 5000 in increments of 1000. The bars labeled on thex-axis correspond to, from left to right: ADA6.0, ADA6.5, ADA7.0,AMPD8.0, AMPD8.5, BIS-TRIS-propane6.3, BIS-TRIS-propane6.5,BIS-TRIS-propane7.0, BIS-TRIS-propane7.5, BIS-TRIS-propane8.0,BIS-TRIS-propane8.5, BIS-TRIS6.0, BIS-TRIS6.5, BIS-TRIS7.0, DIPSO7.0,DIPSO7.5, DIPSO8.0, HEPES7.0, HEPES7.5, HEPES8.0, MES5.5, MES6.0,MES6.5, MES6.7, MOPS6.5, MOPS7.0, MOPS7.5, MOPS8.0, Nono, PIPES6.1,PIPES6.5, PIPES7.0, PIPES7.5, SPG5.5, SPG6.0, SPG6.5, SPG7.0, SPG7.5,SPG8.0, SPG8.5, TAPS7.7, TAPS8.0, TAPS8.5, TAPSO7.0, TAPSO7.5, TAPSO8.0,TRIS7.1, TRIS7.5, TRIS8.0, TRIS8.5, bioine7.6, bioine8.0, bioine8.5,otrate5.5, otrate6.0, otrate6.5, otrate7.0, glycylglycin7.5,glycylglycin8.0, glycylglycin8.5, midazole6.2, midazole6.5, midazole7.0,midazole7.5, midazole7.8, malsate6.0, malsate6.5, malsate7.0,melonate5.5, melonate6.0, melonate6.5, melonate7.0, melonate7.5,melonate8.0, phosphate6.0, phosphate6.5, phosphate7.0, phosphate7.5,phosphate8.0, succinate5.5, succinate6.0, succinate6.5, tricine7.5,tricine8.0, and tricine8.5.

FIG. 56 shows 12 line plots. All 12 μlots show fluorescence over time.The x-axis of all 16 μlots shows minutes from 0 to 75 in increments of25, and the y-axis shows raw fluorescence (AU) from 0 to 40,000 inincrements of 10,000. Each plot shows two lines corresponding toactivator concentrations of 1 pM or 0 pM. The plots in the top row showdifferent buffers with no tRNA. The arrangement of the lines in eachplot in the top row, from left to right, are as follows: In the plotshowing NEB1, the line corresponding to 1 pM rises very slightly overtime, and the line corresponding to 0 pM appears approximately flat. Inthe plot showing NEB2, the line corresponding to 1 pM rises slightlyover time, and the line corresponding to 0 pM appears approximatelyflat. In the plot showing NEB3, the line corresponding to 1 pM risesvery slightly over time, and the line corresponding to 0 pM appearsapproximately flat. In the plot showing CutSmart, the line correspondingto 1 pM rises over time, and the line corresponding to 0 pM appearsapproximately flat. In the plot showing RNPB, both lines appearapproximately flat. In the plot showing Normal, the line correspondingto 1 pM rises slightly over time, and the line corresponding to 0 pMrises slightly over time but remains below the line corresponding to 1pM. The plots in the bottom row show different buffers with tRNA. Thearrangement of the lines in each plot in the bottom row, from left toright, are as follows: In the plot showing NEB1, both lines appearapproximately flat. In the plot showing NEB2, the line corresponding to1 pM rises slightly over time, and the line corresponding to 0 pMappears approximately flat. In the plot showing NEB3, the linecorresponding to 1 pM rises very slightly over time, and the linecorresponding to 0 pM appears approximately flat. In the plot showingCutSmart, the line corresponding to 1 pM rises over time, and the linecorresponding to 0 pM appears approximately flat. In the plot showingRNPB, both lines appears approximately flat. In the plot showing Normal,the line corresponding to 1 pM rises slightly over time, and the linecorresponding to 0 pM rises slightly over time but remains below theline corresponding to 1 pM.

FIG. 57 shows a bar plot depicting fluorescence at differentconcentrations. The y-axis shows background subtracted fluorescence from0 to 60,000 in increments of 10,000. The bar plot shows six sets of twobars. The six sets correspond to, from left to right, 100 pM, 10 pM, 1pM, 100 fM, 10 fM, and 0. Each set of two bars shows original buffer onthe left and MBuffer 1 on the right. At 100 pM, the MBuffer1 bar isslightly higher than the original buffer bar. At 10 pM and 1 pM, theMBuffer1 bar is much higher than the original buffer bar. The originalbuffer bar is not visible at 100 fM, 10 fM or 0. The MBuffer1 bar is notvisible at 0.

FIG. 60 shows a bar graph of Lbu-Cas13a—additive screen. The y-axisshows background subtracted fluorescence (AU) from 0 to 50,000 inincrements of 10,000. The bars labeled on the x-axis correspond to, fromleft to right: 0.00 M no-treatment, 1.00% w/v Polyvinyl alcohol TypeIII, 1.00 M 1, 2, 3 hexemetriol, 1.00 M Ammonium formate, 1.00 MBenzamidine hydrochloride, 1.00 M Beryllium sulfate, 1.00 M Cesiumchloride, 1.00 M D-*(+I-Glucose, 1.00 M D-(+1-Marinose, 1.00 MD-(+1-Sucrose, 1.00 M D-(+-Trehalose, 1.00 M D-I-1-Fructose, 1.00 MD-Sorbitol, 1.00 M Glycine, 1.00 M L.-Proline, 1.00 M Manganese (II)chloride, 1.00 M Polyethylene glycol 200, 1.00 M Potassium acetate, 1.00M Potassium bromide, 1.00 M Potassium chloride, 1.00 M Potassium iodide,1.00 M Potassium nitrate, 1.00 M Pyridine, 1.00 M Rubidium chloride,1.00 M Sodium iodide, 1.00 M Urea, 1.00 M Zinc chloride, 1.00 Mdi-Ammonium hydrogen phosphate, 1.00 M tri-Lithium citrate, 1.8 Mtri-Sodium citrate, 100 mM 2-Aminceathanesulfonic acid, 100 mMAdenosine-5′-triphosphate disodium salt, 100 mM Barium chloride, 100 mMBetaine, 100 mM Cadmium chloride, 100 mM Cobalt (II) chloride, 100 mMCooper (II) chloride, 100 mM Dithiothreitol, 100 mM Ectoine, 100 mMEthylenediaminetetraacetic acid disodium salt, 100 mM L-Cysteine, 100 mMPhenol, 100 mM Spermidine trihydrochloride, 100 mM Strontium chloride,100 mM Yttrium (III) chloride, 2.00 M 1.6-Diaminohexane, 2.00 M1.8-Diaminooctane, 2.00 M 6-Aminohexanoic acid, 2.00 M Adonitol, 2.00 MAmmonium bromide, 2.00 M Ammonium chloride, 2.00 M Ammonium fluoride,2.00 M Ammonium nitrate, 2.00 M Ammonium sulfate, 2.00 M Ammoniumthiocyanate, 2.00 M Ammonium trifluoroacetate, 2.00 M Erythritol, 2.00 MEthanolamine, 2.00 M Glycerol, 2.00 M Guanidine hydrochloride, 2.00 MLithium acetate, 2.00 M Lithium bromide, 2.00 M Lithium chloride, 2.00 MLithium nitrite, 2.00 M Lithium perchlorate, 2.00 M Lithium salicylate,2.00 M Lithium sulfate, 2.00 M Magnesium sulfate, 2.00 M PotassiumCyanate, 2.00 M Potassium thiocyanate, 2.00 M Sodium bromide, 2.00 MSodium fluoride, 2.00 M Sodium nitrate, 2.00 M Sodium perchlorate, 2.00M Sodium sulfate, 2. μN Sodium thiocynate, 2.00 M Sodiumtrichloroacetate, 2.00 M Tetramethylammonium Chloride, 2.00 MTrimethylamine hydrochloride, 2.00 M Xylitol, 2.00 M di-Ammoniumtartrate, 2.00 M di-Sodium malonate, 20.00 mM Dextran sulfate sodiumsalt 5,000, 200 mM Aluminum chloride, 200 mM Calcium chloride, 200 mMMagnesium chloride, 300 mM Glycyl-glycyl-glycine, 4.00 M Dimethylsulfoxide, 4.00 M Dimethylformamide, 5.00%. w/v PolyvinylpyrrolidoneK15, 500 mM Lactose, 500 mM Polyethylene glycol 600, 500 mMPolypropylene glycol 400, 500 mM e-Caprolactam, 600 mM Potassiumsulfate, and 800 mM Mannitol.

FIG. 61 shows a bar graph of Cas12a buffer optimization—take 1, 45minutes, 0.1 nM activator. The y-axis shows background subtractedfluorescence (AU) from 0 to 17500 in increments of 2500. The barslabeled on the x-axis correspond to, from left to right: ADA6.0, ADA6.5,ADA7.0, AMPD8.0, AMPD8.5, BIS-TRIS-propane6.3, BIS-TRIS-propane6.5,BIS-TRIS-propane7.0, BIS-TRIS-propane7.5, BIS-TRIS-propane8.0,BIS-TRIS-propane8.5, BIS-TRIS6.0, BIS-TRIS6.5, BIS-TRIS7.0, DIPSO7.0,DIPSO7.5, DIPSO8.0, HEPES7.0, HEPES7.5, HEPES8.0, MES5.5, MES6.0,MES6.5, MES6.7, MOPS6.5, MOPS7.0, MOPS7.5, MOPS8.0, Nono, PIPES6.1,PIPES6.5, PIPES7.0, PIPES7.5, SPG5.5, SPG6.0, SPG6.5, SPG7.0, SPG7.5,SPG8.0, SPG8.5, TAPS7.7, TAPS8.0, TAPS8.5, TAPSO7.0, TAPSO7.5, TAPSO8.0,TRIS7.1, TRIS7.5, TRIS8.0, TRIS8.5, bioine7.6, bioine8.0, bioine8.5,otrate5.5, otrate6.0, otrate6.5, otrate7.0, glycylglycin7.5,glycylglycin8.0, glycylglycin8.5, midazole6.2, midazole6.5, midazole7.0,midazole7.5, midazole7.8, malsate6.0, malsate6.5, malsate7.0,melonate5.5, melonate6.0, melonate6.5, melonate7.0, melonate7.5,melonate8.0, phosphate6.0, phosphate6.5, phosphate7.0, phosphate7.5,phosphate8.0, succinate5.5, succinate6.0, succinate6.5, tricine7.5,tricine8.0, and tricine8.5.

FIG. 62 shows eight line plots. All eight plots show fluorescence overtime. The x-axis of all eight plots shows minutes from 0 to 80 inincrements of 20, and the y-axis shows raw fluorescence (AU) from 0 to5000 in increments of 1000. Each plot shows two lines corresponding toconcentrations of 0.01 or 0. The arrangement of the lines in each plotin the top row, from left to right, are as follows: In the plot showing0 mM KCl, 10 pM activator, the line corresponding to 0.01 rises overtime, and the line corresponding to 0 appears approximately flat. In theplot showing 20 mM KCl, 10 pM activator, the line corresponding to 0.01rises over time, and the line corresponding to 0 rises slightly overtime but remains lower than the line corresponding to 0.01. In the plotshowing 40 mM KCl, 10 pM activator, the line corresponding to 0.01 risesover time, and the line corresponding to 0 rises slightly over time butremains lower than the line corresponding to 0.01. In the plot showing80 mM KCl, 10 pM activator, the line corresponding to 0.01 rises overtime, and the line corresponding to 0 slightly over time but remainslower than the line corresponding to 0.01. In the plot showing 160 mMKCl, 10 pM activator, both lines appear approximately flat. In the plotshowing 320 mM KCl, 10 pM activator, both lines appear approximatelyflat. In the plot showing 640 mM KCl, 10 pM activator, both lines appearapproximately flat. In the plot showing 1280 mM KCl, 10 pM activator,both lines appear approximately flat.

FIG. 63 shows a bar graph of Cas12M08—additive screen. The y-axis showsbackground subtracted fluorescence (AU) from 0 to 5000 in increments of1000. The bars labeled on the x-axis correspond to, from left to right:1.25×BufferLessMM, ADA6.0, ADA6.5, ADA7.0, AMPD8.0, AMPD8.5,BIS-TRIS-propane6.3, BIS-TRIS-propane6.5, BIS-TRIS-propane7.0,BIS-TRIS-propane7.5, BIS-TRIS-propane8.0, BIS-TRIS-propane8.5,BIS-TRIS6.0, BIS-TRIS6.5, BIS-TRIS7.0, CIPSO7.0, CIPSO7.5, CIPSO8.0,HEPES7.0, HEPES7 5, HEPES8.0, MES5.5, MES6.0, MES6.5, MES6.7, MOPS6.5,MOPS7.0, MOPS7.5, MOPS8.0, PIPES6.1, PIPES6.5, PIPES7.0, PIPES7.5,SPG5.5, SPG6.0, SPG6.5, SPG7.0, SPG7.5, SPG8.0, SPG8.5, TAPS7.7,TAPS8.0, TAPS8.5, TAPSO7.0, TAPSO7.5, TAPSO8.0, TRIS7.1, TRIS7.5, TRIS80, TRIS8.5, bicine7.0, bicine8.0, bicine8.5, citrate5.5, citrate6.0,citrate 6.5, citrate7.0, glycylglycine7.5, glycylglycine8.0,glycylglycine8.5, irridazole6.2, irridazole6.5, irridazole7.0,irridazole7.5, irridazole7.8, maleate6.0, maleate6.5, maleate7.0,malonate5.5, malonate6.0, malonate6.5, malonate7.0, malonate7.5,malonate8.0, phosphate6.0, phosphate6.5, phosphate7.0, phosphate7.5,phosphate8.0, succinate5.5, succinate6.0, succinate6.5, tricine7.5,tricine8.0, and tricine8.5.

FIG. 64 shows a bar plot depicting fluorescence at different salt typesand concentrations. The y-axis shows background subtracted fluorescencefrom 0 to 15,000 in increments of 2,500. The bar plot shows eight setsof two bars. The eight sets correspond to salt concentrations (mM) of,from left to right, 0.0, 1.88, 3.75, 7.5, 15.0, 30.0, 60.0, and 120.0.Each set of two bars shows C1 on the left and Acetate.

FIG. 66 shows a bar graph of Cas12M08—additive screen. The y-axis showsbackground subtracted fluorescence (AU) from 0 to 25,000 in incrementsof 5,000. The bars labeled on the x-axis correspond to, from left toright: 0.00M no-treatment, 1.00% w/v Polyvinyl alcohol Type II, 1.00 M1,2,3-hexanetriol, 1.00 M Ammonium formate, 1.00 M Benzamidinehydrochloride, 1.00 M Beryllium sulfate, 1.00 M Ceslum chloride, 1.00 MD-(+)-Glucose, 1.00 M D-(+)-Mannose, 1.00 M D-(+)-Sucrose, 1.00 MD-(+)-Trehalose, 1.00 M D-(−)-Fructose., 1.00 M D-Sorbitol, 1.00 MGlycine, 1.00 M L-Proline, 1.00 M Manganese (II) chloride, 1.00 MPolythylene glycol 200, 1.00 M Potassium acetate, 1.00 M Potassiumbromide, 1.00 M Potassium chloride, 1.00 M Potassium iodide, 1.00 MPotassium nitrate, 1.00 M Pyridine, 1.00 M Rubidium chloride, 1.00 MSodium iodide, 1.00 M Trimethylamine N-oxide, 1.00 M Urea, 1.00 M Zincchloride, 1.00 M di-Ammonium hydrogen phosphate, 1.00 M tri-Lithiumcitrate, 1.8 M tri-Sodium citrate, 100 mM 2-Aminoethanesulfonic acid,100 mM Adonosine-5′-triphosphate disodium salt, 100 mM Barium chloride,100 mM Betaine, 100 mM Cadmium chloride, 100 mM Cobalt (II) chloride,100 mM Copper (II) chloride, 100 mM Dithiothreitol, 100 mM Ectoine, 100mM Ethylenediaminetetraacetic acid disodum salt, 100 mM L-Cysteine, 100mM Phenol, 100 mM Spermidine trihydrochloride, 100 mM Strontiumchloride, 100 mM Yttrium (III) chloride, 2.00 M 1.6-Diaminohexane, 2.00M 1.8-Diaminooctane, 2.00 M 6-Aminohexanoic acid, 2.00 M Adonitol, 2.00M Ammonium bromide, 2.00 M Ammonium chloride, 2.00 M Ammonium fluoride,2.00 M Ammonium nitrate, 2.00 M Ammonium sulfate, 2.00 M Ammoniumthiocyanate, 2.00 M Ammonium trifluoroacetate, 2.00 M Erythritol, 2.00 MEthanolamine, 2.00 M Glycerol, 2.00 M Guanidine hydrochloride, 2.00 MLithium acetate, 2.00 M Lithium bromide, 2.00 M Lithium chloride, 2.00 MLithium nitrate, 2.00 M Lithium perchlorate, 2.00 M Lithium salicylate,2.00 M Lithium sulfate, 2.00 M Magnesium sulfate, 2.00 M PotassiumCyanate, 2.00 M Potassium thiocyanate, 2.00 M Sodium bromide, 2.00 MSodium fluoride, 2.00 M Sodium nitrate, 2.00 M Sodium perchlorate, 2.00M Sodium sulfate, 2.00 M Sodium thiocyanate, 2.00 M Sodiumtrichloroacetate, 2.00 M Tetramethylammonium Chloride, 2.00 MTrimethylamine hydrochloride, 2.00 M Xylitol, 2.00 M di-Ammoniumtartrate, 2.00 M di-Sodium malonate, 20.00 mM Dextran sulfate sodiumsalt 5,000, 200 mM Aluminium chloride, 200 mM Calcium chloride, 200 mMMagnesium chloride, 300 mM Glycyl-glycyl-glycine, 4.00 M Dimethylsulfoxide, 4.00 M Dimethylformamidele, 5.00% w/v PolyvinylpyrrolidoneK15, 500 mM Lactose, 500 mM Polyethylene glycol 600, 500 mMPolypropylene glycol 400, 500 mM e-Caprolactarn, 600 mM Potassiumsulfate, and 800 mM Mannitol.

FIG. 93C shows six line plots depicting fluorescence over time. In allsix plots the x-axis shows minutes from 0 to 75 in increments of 25, andthe y-axis shows normalized fluorescence from 0.0 to 1.0 in incrementsof 0.2. Each plot depicts two sets of four lines. The first set of fourlines shows concentrations (nM) of 2.5, 0.25, 0.025, and 0 with anRNA-FQ reporter (solid lines). The second set of four lines showsconcentrations (nM) of 2.5, 0.25, 0.025, and 0 with an DNA-FQ reporter(dashed lines). The top left plot shows target=RNA, protein=Cas13M26.The lines corresponding to 2.5 RNA-FQ, 0.25 RNA-FQ, and 0.0025 RNA-FQrise over time. The line corresponding to 2.5 RNA-FQ is the highest,followed by the line corresponding to 0.25 RNA-FQ, and the linecorresponding to 0.025 RNA-FQ is the lowest of the three. The remaininglines are not distinguishable from the baseline. The top middle plotshows target=ssDNA, protein=Cas13M26. The lines corresponding to 2.5RNA-FQ and 0.25 RNA-FQ rise over time. The line corresponding to 2.5RNA-FQ is the highest, followed by the line corresponding to 0.25RNA-FQ. The remaining lines are not distinguishable from the baseline.The top right plot shows target=dsDNA, protein=Cas13M26. None of thelines are distinguishable from baseline. The bottom left plot showstarget=RNA, protein=Cas12M08. None of the lines are distinguishable frombaseline. The bottom middle plot shows target=ssDNA, protein=Cas12M08.The lines corresponding to 2.5 DNA-FQ, 0.25 DNA-FQ, and 0.0025 DNA-FQrise over time. The line corresponding to 2.5 DNA-FQ is the highest,followed by the line corresponding to 0.25 DNA-FQ, and the linecorresponding to 0.025 DNA-FQ is the lowest of the three. The remaininglines are minimally distinguishable from the baseline. The bottom rightplot shows target=dsDNA, protein=Cas12M08. The lines corresponding to2.5 DNA-FQ, 0.25 DNA-FQ, and 0.0025 DNA-FQ rise over time. The linecorresponding to 2.5 DNA-FQ is the highest, followed by the linecorresponding to 0.25 DNA-FQ, and the line corresponding to 0.025 DNA-FQis the lowest of the three. The remaining lines are minimallydistinguishable from the baseline.

FIG. 94 shows two line plots depicting fluorescence over time. For bothplots, the x-axis shows minutes from 0 to 50 in increments of 50, andthe y-axis shows raw fluorescence (AU) from 0 to 2,000,000 in incrementsof 500,000. Both plots depict lines representing the reportersrep01—FAM-U5, rep08—A5, rep09—C5, rep10—G5, rep 11—T5, rep12—TA6,rep13—TA13, rep14—TA10, rep15—T6, rep16—T7, rep19—T10, rep20—T11,rep21-T12, and rep30—beacon. The left plot shows 0 nM, and none of thelines are substantially distinguishable from baseline. The right plotshows 2.5 nM. The line corresponding to rep01—FAM-up rise over time. Theremaining lines are not substantially distinguishable from baseline.

FIG. 98A shows a bar plot depicting fluorescence with different crRNAand primers. The y-axis shows normalized fluorescence from 0 to 160,000in increments of 20,000. The x-axis shows crRNA. The plot depicts twosets of three bars. The left set depicts on-target crRNA, and the rightset depicts off-target crRNA. The three bars in each set correspond tothe primers, from left to right, LF+LB, LF, and LB.

FIG. 105 shows a line graph depicting fluorescence over time produced bya Cas12 DETECTR reaction in the presence of different volumes of LAMPamplicon per DETECTR reaction. The x-axis shows time in minutes from 1to 10 in increments of 2. The y-axis shows raw fluorescence (AU) from 0to 40,000 in increments of 5000. Fluorescence over time is plotted for 0μL, 2 μL, 4 μL, 6 μL, 8 μL, 10 μL, 12 μL, or 14 μL of LAMP amplicon.Fluorescence increases over time for reactions containing 2 μL, 4 μL, 6μL, 8 μL, 10 μL, or 12 μL LAMP amplicon. The line corresponding 2 μL isthe highest, followed by the line corresponding to 4 μL, then the linecorresponding to 6 μL, 8 μL, then the line corresponding to 10 μL, thenthe line corresponding to 12 μL. The lines corresponding to 0 μL and 14μL do not rise perceptibly above baseline.

While various embodiments of the present invention have been shown anddescribed herein, it will be apparent to those skilled in the art thatsuch embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the invention. It should be understoodthat various alternatives to the embodiments of the invention describedherein may be employed in practicing the invention. It is intended thatthe following claims define the scope of the invention and that methodsand structures within the scope of these claims and their equivalents becovered thereby.

NUMBERED EMBODIMENTS

The following embodiments recite non-limiting permutations ofcombinations of features disclosed herein. Other permutations ofcombinations of features are also contemplated. In particular, each ofthese numbered embodiments is contemplated as depending from or relatingto every previous or subsequent numbered embodiment, independent oftheir order as listed. 1. A system for detecting a target nucleic acid,said system comprising: a) a support medium; b) a guide nucleic acidtargeting a target sequence; c) a programmable nuclease capable of beingactivated when complexed with the guide nucleic acid and the targetsequence; and d) a single stranded detector nucleic acid comprising adetection moiety, wherein the detector nucleic acid is capable of beingcleaved by the activated nuclease, thereby generating a first detectablesignal. 2. A system for detecting a target nucleic acid comprising: a) areagent chamber comprising: 1) a guide nucleic acid targeting a targetsequence; 2) a programmable nuclease capable of being activated whencomplexed with the guide nucleic acid and the target sequence; and 3) asingle stranded detector nucleic acid comprising a detection moiety,wherein the detector nucleic acid is capable of being cleaved by theactivated nuclease, thereby generating a first detectable signal; and b)a support medium for detection of the first detectable signal. 3. A kitfor detecting a target nucleic acid in a sample comprising: a) a supportmedium; b) a guide nucleic acid targeting a target sequence; c) aprogrammable nuclease capable of being activated when complexed with theguide nucleic acid and the target sequence; and d) a single strandeddetector nucleic acid comprising a detection moiety, wherein thedetector nucleic acid is capable of being cleaved by the activatednuclease, thereby generating a first detectable signal. 4. A method ofdetecting a target nucleic acid in a sample comprising: a) contactingthe sample with 1) a guide nucleic acid targeting a target sequence; 2)a programmable nuclease capable of being activated when complexed withthe guide nucleic acid and the target sequence; 3) a single strandeddetector nucleic acid comprising a detection moiety, wherein thedetector nucleic acid is capable of being cleaved by the activatednuclease, thereby generating a first detectable signal; and b)presenting the first detectable signal using a support medium. 5. Asupport medium comprising: a) a guide nucleic acid targeting a targetsequence on a surface of the support medium; b) a programmable nucleasecapable of being activated when complexed with the guide nucleic acidand the target sequence on the surface of the support medium; c) asingle stranded detector nucleic acid comprising a detection moiety,wherein the detector nucleic acid is capable of being cleaved by theactivated nuclease, thereby generating a first detectable signal; and d)a biological sample on the support medium. 6. A method of detecting atarget nucleic acid in a sample comprising: a) contacting the samplecomprising the target nucleic acid with 1) a guide nucleic acidtargeting a target sequence; 2) a programmable nuclease capable of beingactivated when complexed with the guide nucleic acid and the targetsequence; and 3) a single stranded detector nucleic acid comprising adetection moiety, wherein the detector nucleic acid is capable of beingcleaved by the activated nuclease, thereby generating a first detectablesignal; b) cleaving the single stranded detector nucleic acid using theprogrammable nuclease that cleaves with an efficiency of 50% as measuredby a change in color; and c) measuring the first detectable signal on asupport medium. 7. The system, kit, method, or support medium any one ofembodiments 1-6, wherein the support medium comprises a lateral flowassay device. 8. The system, kit, method, or support medium any one ofembodiments 1-6, wherein the support medium comprises nitrocellulose. 9.The system, kit, method, or support medium any one of embodiments 1-6,wherein the support medium comprises cellulose. 10. The system, kit,method, or support medium any one of embodiments 1-6, wherein thesupport medium is a PCR plate or a PCR subset plate. 11. The system,kit, method, or support medium of embodiment 10, wherein the PCR platehas 96 wells or 384 wells. 12. The system, kit, method, or supportmedium of embodiment 10, wherein the PCR plate or PCR subset plate ispaired with a fluorescent light reader, a visible light reader, or amobile device. 13. The system, kit, method, or support medium ofembodiment 5, wherein the support medium comprises a sample pad region,a conjugate pad region, a detection region, and an absorbent pad region.14. The system, kit, method, or support medium of embodiment 13, whereinthe conjugate pad region comprises a conjugate, wherein the conjugatecomprises a nanoparticle, a gold nanoparticle, a latex nanoparticle, ora quantum dot. 15. The system, kit, method, or support medium ofembodiment 13, wherein the conjugate comprises a conjugate bindingmolecule attached to a surface of the conjugate. 16. The system, kit,method, or support medium any one of embodiments 1-6, wherein thedetection moiety comprises a fluorescent dye. 17. The system, kit,method, or support medium of embodiment 1-6, wherein the detectionmoiety comprises a fluorescence resonance energy transfer (FRET) pair.18. The system or method any one of embodiments 1-6, wherein thedetection moiety comprises a polypeptide. 19. The system, kit, method,or support medium of any one of embodiments 1-6, wherein the detectionmoiety comprises a biotin. 20. The system, kit, method, or supportmedium of any one of embodiments 1-6, wherein the detection moietycomprises a polysaccharide, a polymer, or a nanoparticle. 21. Thesystem, kit, method, or support medium of embodiment 15, wherein theconjugate binding molecule binds the detection moiety. 22. The system,kit, method, or support medium of embodiment 21, wherein the conjugatebinding molecule binds selectively to the detection moiety cleaved fromthe detector nucleic acid. 23. The system, kit, method, or supportmedium of embodiment 15, wherein the conjugate binding moleculecomprises an antibody or a fragment of an antibody. 24. The system, kit,method, or support medium of embodiment 15, wherein the conjugatebinding molecule comprises avidin or a polypeptide that binds biotin.25. The system, kit, method, or support medium of embodiment 15, whereinthe conjugate binding molecule comprises a detector moiety bindingnucleic acid. 26. The system, kit, method, or support medium ofembodiment 13, wherein the detection region comprises a capturemolecule, wherein the capture molecule is capable of binding to thedetection moiety, and a control capture molecule. 27. The system, kit,method, or support medium of embodiment 26, wherein the control capturemolecule is capable of binding to a molecule in the sample, detectionmoiety on an uncleaved detection nucleic acid, or a molecule from theconjugate pad region. 28. The system or method of embodiment 26, whereinthe capture molecule and the control capture molecule are located inspatially distinct regions on the detection region. 29. The system, kit,method, or support medium of embodiment 26, wherein the capture moleculebinds the detection moiety. 30. The system, kit, method, or supportmedium of embodiment 29, wherein the capture molecule comprises anantibody or a fragment of an antibody. 31. The system, kit, method, orsupport medium of embodiment 29, wherein the first detection signal isgenerated by binding of the detection moiety to the capture molecule inthe detection region, wherein the first detection signal indicates thatthe sample contained the target nucleic acid. 32. The system, kit,method, or support medium any one of embodiments 1-6, wherein the systemis capable of detecting more than one type of target nucleic acid,wherein the system comprises more than one type of guide nucleic acidand more than one type of detector nucleic acid. 33. The system, kit,method, or support medium any one of embodiments 1-6, wherein thedetection of the detectable signal by the support medium increases withcleaving of the detector nucleic acid. 34. The system, kit, method, orsupport medium any one of embodiments 1-6, wherein the detection of thedetectable signal by the support medium decrease with cleaving of thedetector nucleic acid. 35. The system, kit, method, or support medium ofany one of embodiments 1-6, wherein the detectable signal is generateddirectly by the cleavage event. 36. The system, kit, method, or supportmedium of any one of embodiments 1-6, wherein the detectable signal isgenerated indirectly by the signal event. 37. The system, kit, method,or support medium of any one of embodiments 1-6, wherein a second targetnucleic acid is detected on the same support medium. 38. The system,kit, method, or support medium of embodiment 37, wherein the secondtarget nucleic acid is targeted by a second guide nucleic acid. 39. Thesystem, kit, method, or support medium of embodiment 37, wherein secondtarget nucleic acid is targeted by a second programmable nucleic acid.40. The system, kit, method, or support medium of embodiment 37, whereinactivation of nuclease upon complexing with the second target nucleicacid generates a second detectable signal from a second detectionnucleic acid comprising a second detection moiety. 41. The system, kit,method, or support medium of embodiment 40, wherein the seconddetectable signal is different from the first detectable signal. 42. Thesystem, kit, method, or support medium of embodiment 37, wherein thesecond target nucleic acid is a related serotype or variant of the firsttarget nucleic acid. 43. The system, kit, method, or support medium ofembodiment 37, wherein the system allows multiplexing and detection ofmultiple target nucleic acids on a single support medium. 44. Thesystem, kit, method, or support medium of embodiment 43, wherein thereis a guide nucleic acid specific for each of the multiple target nucleicacids. 45. The system, kit, method, or support medium of embodiment 43,wherein a conjugate pad of the support medium comprises a conjugate witha first and a second conjugate binding molecules attached to a surfaceof the conjugate, wherein the first and the second conjugate bindingmolecules bind to the a first and a second detection moieties,respectively. 46. The system, kit, method, or support medium ofembodiment 43, wherein a conjugate pad of the support medium comprises afirst conjugate with a first conjugate binding molecule, and a secondconjugate with a second conjugate binding molecule, wherein the firstand the second conjugate binding molecules bind to the a first and asecond detection moieties, respectively. 47. The system, kit, method, orsupport medium of embodiments 45 or 46, wherein the conjugate comprisesa nanoparticle, a gold nanoparticle, a latex nanoparticle, or a quantumdot. 48. The system, kit, method, or support medium of embodiment 47,wherein a detection region of the support medium comprises spatiallydistinct regions for a first capture molecule and a second capturemolecule, wherein the first and second capture molecules bind to firstand a second detection moieties, respectively. 49. The system, kit,method, or support medium of embodiment 47, wherein the seconddetectable signal is generated in a spatially distinct location than thefirst generated signal. 50. The system, kit, method, or support mediumof embodiment 47, wherein the detected target nucleic acid is identifiedbased on its spatial location on the detection region of the supportmedium. 51. The system, kit, method, or support medium of embodiment 47,wherein a detection region of the support medium comprises a spatiallyidentical region for a first capture molecule and a second capturemolecule, wherein the first and second capture molecules bind to firstand a second detection moieties, respectively. 52. The system, kit,method, or support medium of any one of embodiments 1-6, wherein thedetectable signal is not a fluorescent signal. 53. The system, kit,method, or support medium of any one of embodiments 1-6, wherein thedetectable signal is a colorimetric or color-based signal. 54. Thesystem, kit, method, or support medium of any one of embodiments 1-6,wherein the support medium comprises a barcode. 55. The system, kit,method, or support medium of embodiment 54, wherein the barcode can bescanned using a camera with a mobile application. 56. The system, kit,method, or support medium of any one of embodiments 1-6, wherein thesupport medium comprises a reference color guide. 57. The system, kit,method, or support medium of embodiment 56, wherein the reference colorguide can be scanned using a camera with a mobile application. 58. Thesystem, kit, method, or support medium of any one of embodiments 1-6,wherein the target nucleic acid is amplified prior to contacting it tothe support medium. 59. The system, kit, method, or support medium ofembodiment 58, wherein the amplification is isothermal amplification.60. The system, kit, method, or support medium of embodiment 59, whereinthe amplification comprises isothermal recombinase polymeraseamplification (RPA), transcription mediated amplification (TMA), stranddisplacement amplification (SDA), helicase dependent amplification(HDA), loop mediated amplification (LAMP), rolling circle amplification(RCA), single primer isothermal amplification (SPIA), ligase chainreaction (LCR), simple method amplifying RNA targets (SMART), orimproved multiple displacement amplification (IMDA). 61. The system,kit, method, or support medium of any one of embodiments 1-6, whereinthe sample is transferred onto the support medium. 62. The system, kit,method, or support medium of embodiment 61, wherein the transfer occursautomatically or semi-automatically in situ. 63. The system, kit,method, or support medium of any one of embodiments 1-6, wherein thesupport medium is placed into a reagent chamber holding the sample. 64.The system, kit, method, or support medium of any one of embodiments1-6, wherein the target nucleic acid is not amplified prior tocontacting the support medium. 65. The system, kit, method, or supportmedium of any one of embodiments 1-6, wherein the programmable nucleaseis Cas13. 66. The system, kit, method, or support medium of embodiment65, wherein Cas13 is Cas13a, Cas13b, Cas13c, Cas13d, or Cas13e. 67. Thesystem, kit, method, or support medium of one of embodiments 1-6,wherein the programmable nuclease is Cas12. 68. The system, kit, method,or support medium of embodiment 67, wherein the Cas12 is Cas12a, Cas12b,Cas12c, Cas12d, or Cas12e. 69. The system, kit, method, or supportmedium of embodiments 1-6, wherein the programmable nuclease is Csm1,Cas9, C2c4, C2c8, C2c5, C2c10, C2c9, or casZ. 70. The system, kit,method, or support medium of any one of embodiments 1-6, wherein theguide nucleic acid targeting a target sequence is selected from a groupof tiled guide nucleic acids that bind to a nucleic acid of a strain ofan infection. 71. The system, kit, method, or support medium of any oneof embodiments 1-6, wherein the guide nucleic acid targeting a targetsequence is selected from a group of tiled guide nucleic acids that bindto a nucleic acid of a strain of HPV 16 or HPV18. 72. The system, kit,method, or support medium of any one of embodiments 1-6, wherein thesample comprises a blood sample, a serum sample, a plasma sample, asaliva sample, a urine sample, a sputum sample, a mucosal sample, aperitoneal fluid sample, a tissue sample, an exudate, an effusion, or acell free DNA sample. 73. The system, kit, method, or support medium ofany one of embodiments 1-6, wherein the sample comprises a non-humananimal sample. 74. The system, kit, method, or support medium of any oneof embodiments 1-6, wherein the sample comprises a plant sample, afungal sample, a bacterial sample, or a viral sample. 75. The system,kit, method, or support medium of any one of embodiments 1-6, whereinthe sample comprises a soil sample, or an environmental sample. 76. Thesystem, kit, method, or support medium of any one of embodiments 1-6,wherein the guide nucleic acid comprises a nucleic acid capable ofdetecting HIV, HPV, chlamydia, gonorrhea, syphilis, trichomoniasis,sexually transmitted infection, malaria, Dengue fever, ebola,chikungunya, leishmaniasis, or combinations thereof. 77. The system,kit, method, or support medium of any one of embodiments 1-6, whereinthe sample comprises a human sample. 78. The system, kit, method, orsupport medium of any one of embodiments 1-6, wherein the guide nucleicacid comprises a nucleic acid capable of detecting a gene. 79. Thesystem, kit, method, or support medium of any one of embodiments 78,wherein the gene is expressed or over expressed in a cancer or isexpressed in a genetic disorder. 80. The system, kit, method, or supportmedium of any one of embodiments 1-6, wherein the single strandeddetector nucleic acid comprises: 1) a nucleic acid comprising at leasttwo nucleotides, 2) a fluorophore, and 3) a fluorescence quencher,wherein the fluorophore and the fluorescence quencher are linked by thenucleic acid. 81. The system, kit, method, or support medium of any oneof embodiments 1-6, wherein the single stranded detector nucleic acidcomprises: 1) a nucleic acid comprising at least 3 unmodifiednucleotides, wherein at least two nucleotides are unmodifiedribonucleotides and at least one nucleotide is an unmodifieddeoxyribonucleotide; 2) a fluorophore, and 3) a fluorescence quencher,wherein the fluorophore and the fluorescence quencher are linked by thenucleic acid. 82. The system, kit, method, or support medium of any oneof embodiments 1-6, wherein the single stranded detector nucleic acidcomprises: 1) a nucleic acid comprising at least 3 unmodifiednucleotides, wherein at least two unmodified nucleotides are unmodifieduracil ribonucleotides and at least one nucleotide is an unmodifieddeoxyribonucleotide; 2) a fluorophore, and 3) a fluorescence quencher,wherein the fluorophore and the fluorescence quencher are linked by thenucleic acid. 83. The system, kit, method, or support medium ofembodiment 80, wherein the at least two nucleotides are at least twouracil ribonucleotides. 84. The system, kit, method, or support mediumof embodiment 80, wherein the fluorophore is an infrared fluorescentmoiety. 85. The system, kit, method, or support medium of embodiment 80,wherein the nucleic acid comprises 5 nucleotides, 8 nucleotides, or 10nucleotides. 86. The system, kit, method, or support medium ofembodiment 80, wherein the fluorophore is 5′ 6-FAM and the fluorescencequencher or non-fluorescent fluorescence quencher is 3′ IABkFQ. 87. Thesystem, kit, method, or support medium of embodiment 80, wherein thefluorophore is 5′ 5IRD700 and the fluorescence quencher ornon-fluorescent fluorescence quencher is 3′ IRQC1N. 88. The system, kit,method, or support medium of any one of embodiments 1-6, wherein thesingle stranded detector nucleic acid comprises any one of SEQ ID NO:1—SEQ ID NO: 8. 89. The system, kit, or support medium of any one ofembodiments 1-3, further comprising a biological sample. 90. The system,kit, or support medium of any one of embodiments 1-3, further comprisinga urine sample. 91. The method of embodiment 6, wherein the change incolor is colorimetric signal or a signal visible by eye. 92. The methodof embodiment 6, wherein cleaving the single stranded detector nucleicacid using the programmable nuclease that cleaves with an efficiency of50% as measured by a change in color. 93. The method of embodiment 6,wherein the first detectable signal is detectable within 60 minutes ofthe contacting. 94. The system, kit, method, or support medium of anyone of embodiments 1-6, wherein the single stranded detector nucleicacid is at least one population of the single stranded detector nucleicacid. 95. The system, kit, method, or support medium of any one ofembodiments 1-6, wherein the single stranded detector nucleic acid isany single stranded detector nucleic acid of Table 4. 96. The system,kit, method, or support medium of any one of embodiments 1-6, whereinthe target sequence comprises a single nucleotide polymorphism. 97. Thesystem, kit, method, or support medium of embodiment 96, wherein thesingle nucleotide polymorphism confers resistance to a treatment. 98.The system, kit, method, or support medium of embodiment 97, wherein thetreatment is an antibiotic treatment. 99. A method for detecting atarget nucleic acid, said system comprising: a) providing a sample froma subject; b) introducing the sample into a fluidic device; c)incubating the sample with a pre-complexed Cas mixture in the fluidicsystem in an incubation and detection chamber; and d) generating adetection signal in the fluidic system. 100. The method of embodiment99, wherein prior to step c), the sample is amplified by incubation withamplification mix. 101. The method of embodiment 99, wherein prior tostep b), the sample is filtered using a filtration device for samplepreparation. 102. The method of embodiment 101, wherein the filtrationdevice comprises a narrow tip or glass capillary for collection of thesample. 103. The method of embodiment 102, wherein the filtration devicecomprises a channel to carry the sample. 104. The method of embodiment103, wherein the channel comprises lysis buffer. 105. The method ofembodiment 103, wherein the channel comprises metal, plastic, or abiocompatible material. 106. The method of embodiment 101, wherein thefiltration device further comprises a solution of reagents that willlyse a cell. 107. The method of embodiment 106, wherein the solutioncomprises chaotropic agents, detergents, salts, or any combinationthereof. 108. The method of embodiment 106, wherein the solutioncomprises high osmolality, ionic strength pH, or any combinationthereof. 109. The method of embodiment 1-6, wherein the solutioncomprises a detergent. 110. The method of embodiment 109, wherein thedetergent comprises sodium dodecyl sulphate (SDS) or cetyltrimethylammonium bromide (CTAB). 111. The method of embodiment 99,wherein the fluidic device is manufactured from a plastic polymers,poly-methacrylate (PMMA), cyclic olefin polymer (COP), cyclic olefincopolymer (COC), polyethylene (PE), high-density polyethylene (HDPE),polypropylene (PP), glass, silicon, or any combination thereof. 112. Themethod of embodiment 99, wherein features of the fluidic device orembossed using injection molding, (2) micro-milled or micro-engravedusing computer numerical control (CNC) micromachining, or non-contactlaser drilling (by means of a C02 laser source); (3) incorporated viaadditive manufacturing, and/or (4) incorporated via photolithographicmethods. 113. The method of embodiment 99, wherein the fluidic devicecomprises at least three pumps. 114. The method of embodiment 99,wherein the fluidic device comprises at least three reservoirs. 115. Themethod of embodiment 99, wherein the fluidic device comprises up to fourmicrovalves. 116. The method of embodiment 100, wherein amplificationcomprises loop-mediated isothermal amplification (LAMP), stranddisplacement amplification (SDA), recombinase polymerase amplification(RPA), helicase dependent amplification (HDA), multiple displacementamplification (MDA), rolling circle amplification (RCA), nucleic acidsequence-based amplification (NASBA), or polymerase chain reaction(PCR). 117. The method of embodiment 115, wherein the microvalvescomprise electro-kinetic microvalves, pneumatic microvalves, vacuummicrovalves, capillary microvalves, pinch microvalves, phase-changemicrovalves, or burst microvalves. 118. The method of embodiment 99,wherein after step c), sample, amplification mix, and pre-complexed Casmix are mixed in a serpentine channel and led to a chamber. 119. Themethod of embodiment 118, wherein the chamber is thermoregulated. 120.The method of embodiment 99, wherein the detection signal is generatedby a single stranded detector nucleic acid comprising a detectionmoiety, wherein the detector nucleic acid is capable of being cleaved byan activated nuclease, thereby generating the detectable signal. 121.The method of embodiment 120, wherein the detection signal is detectedby fluorescence, electrochemical detection, or electrochemiluminescence.122. The method of embodiment 99, wherein a fluorimeter is positiondirectly above the incubation and detection chamber. 123. The method ofembodiment 99, wherein the top surface of the incubation and detectionchamber is functionalized with nucleic acid molecules conjugated with abiotin moiety. 124. The method of embodiment 99, wherein the bottomsurface of the incubation and detection chamber operates as an electrodeand is coated with streptavidin molecules. 125. The method of any one ofembodiments 123-124, wherein the pre-complexed Cas mix with an amplifiedtarget nucleic acid flows into the incubation and detection chamber, isactivated at a higher temperature, and cleaves the nucleic acidmolecules conjugated with the biotin moiety. 126. The method ofembodiment 125, wherein the cleaved biotin diffuses to the bottomsurface and binds streptavidin, resulting in an increase in current.127. The method of embodiment 99, wherein an electroactive mediatormoiety conjugated to individual nucleotides of nucleic acid molecules(ssRNA, ssDNA or ssRNA/DNA hybrid molecules) are immobilized on thebottom surface of the incubation and detection chamber. 128. The methodof embodiment 127, wherein the electroactive mediator moiety isferrocene (Fc). 129. The method of embodiment 127, wherein thepre-complexed Cas mix with an amplified target nucleic acid flows intothe incubation and detection chamber, is activated at a highertemperature, and cleaves immobilized Fc-conjugated nucleic acidmolecules, resulting in a decrease in current. 130. The method ofembodiment 99, wherein the incubation and detection chambers areseparate. 131. The method of embodiment 130, wherein a top surface ofthe incubation chamber is coated with ssNA conjugated to invertase. 132.The method of embodiment 130, wherein a bottom surface of the incubationchamber comprises a thin-film planar heater. 133. The method ofembodiment 130, wherein a top surface of the detection chamber comprisesa camera or optical sensor. 134. The method of embodiment 130, wherein abottom surface of the detection chamber comprises a thin-film planarheater. 135. The method of embodiment 132, wherein detection comprisesoptical readout using DNS or electrochemical readout with anelectrochemical analyzer or glucometer. 136. The method of embodiment131, wherein the pre-Complexed Cas mix with an amplified target nucleicacid flows into the incubation and detection chamber, is activated, andcatalyzes breakdown of sucrose to fructose and glucose. 137. The methodof embodiment 136, wherein the amount of fructose and glucose is linkedto a colorimetric reaction. 138. The method of embodiment 136, whereinthe pre-Complexed Cas mix with an amplified target nucleic acid, andglucose flows into a separate chamber wherein the separate chambercomprises glucose oxidase dried on its surface and catalyzes theoxidation of glucose to hydrogen peroxide and D-glucono-δ-lactone. 139.A system for detecting a target nucleic acid by a Cas reaction, saidsystem comprising a fluidic device, wherein the fluidic device comprisesan incubation and detection chamber. 140. The system of embodiment 139,wherein features of the fluidic device or embossed using injectionmolding, (2) micro-milled or micro-engraved using computer numericalcontrol (CNC) micromachining, or non-contact laser drilling (by means ofa C02 laser source); (3) incorporated via additive manufacturing, and/or(4) incorporated via photolithographic methods. 141. The system ofembodiment 139, wherein the fluidic device comprises at least threepumps. 142. The system of embodiment 139, wherein the fluidic devicecomprises at least three reservoirs. 143. The system of embodiment 139,wherein the fluidic device comprises up to four microvalves. 144. Thesystem of embodiment 143, wherein the microvalves compriseelectro-kinetic microvalves, pneumatic microvalves, vacuum microvalves,capillary microvalves, pinch microvalves, phase-change microvalves, orburst microvalves. 145. The system of embodiment 139, wherein the topsurface of the incubation and detection chamber is functionalized withnucleic acid molecules conjugated with a biotin moiety. 146. The systemof embodiment 139, wherein the bottom surface of the incubation anddetection chamber operates as an electrode and is coated withstreptavidin molecules. 147. The system of embodiment 139, wherein anelectroactive mediator moiety conjugated to individual nucleotides ofnucleic acid molecules (ssRNA, ssDNA or ssRNA/DNA hybrid molecules) areimmobilized on the bottom surface of the incubation and detectionchamber. 148. The system of embodiment 147, wherein the electroactivemediator moiety is ferrocene (Fc). 149. The system of embodiment 139,wherein the incubation and detection chambers are separate. 150. Thesystem of embodiment 149, wherein a top surface of the incubationchamber is coated with ssNA conjugated to invertase. 151. The system ofembodiment 149, wherein a bottom surface of the incubation chambercomprises a thin-film planar heater. 152. The system of embodiment 149,wherein a top surface of the detection chamber comprises a camera oroptical sensor. 153. The system of embodiment 149, wherein a bottomsurface of the detection chamber comprises a thin-film planar heater.154. The system of embodiment 149, wherein the fluidic device comprisesa separate chamber comprising glucose oxidase dried on its surface. 155.The method of any one of embodiments 99-138, wherein the pre-complexedCas mixture comprises guide RNA complementary to the target nucleic acidand a Cas protein.

The following embodiments recite permutations of combinations offeatures disclosed herein. In some cases, permutations of combinationsof features disclosed herein are non-limiting. In other casespermutations of combinations of features disclosed herein are limiting.Other permutations of combinations of features are also contemplated. Inparticular, each of these numbered embodiments is contemplated asdepending from or relating to every previous or subsequent numberedembodiment, independent of their order as listed. 1. A system fordetecting a target nucleic acid, said system comprising: a) a supportmedium; b) a guide nucleic acid targeting a target sequence; c) aprogrammable nuclease capable of being activated when complexed with theguide nucleic acid and the target sequence; and d) a single strandeddetector nucleic acid comprising a detection moiety, wherein thedetector nucleic acid is capable of being cleaved by the activatednuclease, thereby generating a first detectable signal. 2. A system fordetecting a target nucleic acid comprising: a) a reagent chambercomprising: 1) a guide nucleic acid targeting a target sequence; 2) aprogrammable nuclease capable of being activated when complexed with theguide nucleic acid and the target sequence; and 3) a single strandeddetector nucleic acid comprising a detection moiety, wherein thedetector nucleic acid is capable of being cleaved by the activatednuclease, thereby generating a first detectable signal; and b) a supportmedium for detection of the first detectable signal. 3. A kit fordetecting a target nucleic acid in a sample comprising: a) a supportmedium; b) a guide nucleic acid targeting a target sequence; c) aprogrammable nuclease capable of being activated when complexed with theguide nucleic acid and the target sequence; and d) a single strandeddetector nucleic acid comprising a detection moiety, wherein thedetector nucleic acid is capable of being cleaved by the activatednuclease, thereby generating a first detectable signal. 4. A method ofdetecting a target nucleic acid in a sample comprising: a) contactingthe sample with 1) a guide nucleic acid targeting a target sequence; 2)a programmable nuclease capable of being activated when complexed withthe guide nucleic acid and the target sequence; 3) a single strandeddetector nucleic acid comprising a detection moiety, wherein thedetector nucleic acid is capable of being cleaved by the activatednuclease, thereby generating a first detectable signal; and b)presenting the first detectable signal using a support medium. 5. Asupport medium comprising: a) a guide nucleic acid targeting a targetsequence on a surface of the support medium; b) a programmable nucleasecapable of being activated when complexed with the guide nucleic acidand the target sequence on the surface of the support medium; c) asingle stranded detector nucleic acid comprising a detection moiety,wherein the detector nucleic acid is capable of being cleaved by theactivated nuclease, thereby generating a first detectable signal; and d)a biological sample on the support medium. 6. A method of detecting atarget nucleic acid in a sample comprising: a) contacting the samplecomprising the target nucleic acid with 1) a guide nucleic acidtargeting a target sequence; 2) a programmable nuclease capable of beingactivated when complexed with the guide nucleic acid and the targetsequence; and 3) a single stranded detector nucleic acid comprising adetection moiety, wherein the detector nucleic acid is capable of beingcleaved by the activated nuclease, thereby generating a first detectablesignal; b) cleaving the single stranded detector nucleic acid using theprogrammable nuclease that cleaves with an efficiency of 50% as measuredby a change in color; and c) measuring the first detectable signal on asupport medium. 7. A system for detecting a target nucleic acid, saidsystem comprising: a support medium; a guide nucleic acid targeting atarget sequence, wherein the guide nucleic acid has a sequence selectedfrom a group of tiled guide nucleic acid that correspond to nucleic acidof a strain of an infectious agent; a programmable nuclease that isactivated when complexed with the guide nucleic acid and the targetsequence; and a single stranded detector nucleic acid comprising adetection moiety, wherein the detectable moiety is detected by adetectable signal upon cleavage by the activated programmable nuclease.8. A system for detecting a target nucleic acid, said system comprising:a support medium; a guide nucleic acid targeting a target sequence; aprogrammable nuclease that is activated when complexed with the guidenucleic acid and the target sequence; and a single stranded detectornucleic acid comprising a detection moiety, wherein the detectablemoiety is detected by a detectable signal upon cleavage by the activatedprogrammable nuclease and wherein the single stranded detector nucleicacid comprises at least 3 nucleotides, wherein at least two nucleotidesare ribonucleotides and at least one nucleotide is adeoxyribonucleotide. 9. A support medium comprising: a first guidenucleic acid targeting a target sequence on a surface of the supportmedium; at least one additional guide nucleic acid targeting a differentportion of the target sequence than the first guide nucleic acid; aprogrammable nuclease that is activated when complexed to the guidenucleic acid and the target sequence on the surface of the supportmedium; a single stranded detector nucleic acid comprising a detectionmoiety, wherein the detectable moiety is detected upon cleavage by theactivated programmable nuclease by a detectable signal; and a biologicalsample on the support medium. 10. A method of detecting a target nucleicacid comprising: contacting a sample comprising a target nucleic acid toa surface of a support medium comprising a programmable nuclease that isactivated when complexed to a guide nucleic acid and the target nucleicacid, and a single stranded detector nucleic acid comprising a detectionmoiety; generating a detectable signal in more than 15 minutes; andassaying for the detection moiety. 11. A method comprising contacting asample to a plurality of programmable sequence specific nucleases,wherein the plurality of programmable nucleases comprises at least oneprogrammable nuclease that is activated when complexed to a guidenucleic acid and a target DNA and at least one programmable nucleasethat is activated when complexed to a guide nucleic acid and a targetRNA, a single stranded detector DNA comprising a first detection moiety,a single stranded detector RNA comprising a second detection moiety; andassaying for the first detection moiety, the second detection moiety, orthe combination thereof. 12. A method of disease assessment in a sample,comprising: a) assaying for a pathogen nucleic acid in the sample usinga first programmable nuclease, and b) assaying for a pathogen resistancelocus in the sample using a second programmable nuclease, wherein thefirst programmable nuclease and the second programmable nuclease do notcleave a common detector nucleic acid site upon activation. 13. A methodof nucleic acid assessment in a sample, comprising a) assaying for afirst nucleic acid in the sample using a first programmable nuclease,and b) assaying for a second nucleic acid in the sample using a secondprogrammable nuclease, wherein the first programmable nuclease and thesecond programmable nuclease do not cleave a common detector nucleicacid site upon activation. 14. A method of circulating nucleic acidquantification, comprising: assaying for a target nucleic acid fromcirculating nucleic acid in a first aliquot of a sample, assaying for acontrol nucleic acid in a second aliquot of the sample, and quantifyingthe target nucleic acid target in the first aliquot by measuring asignal produced by cleavage of a detector nucleic acid. 15. A method ofnucleic acid detection from a raw sample, comprising: protease treatingthe sample for no more than 15 minutes, preamplifying the sample for nomore than 15 minutes, subjecting the sample to a programmablenuclease-mediated detection, and assaying nuclease mediated detection.16. A method of assaying comprising a single assay for a microorganismspecies using a first programmable nuclease and an antibiotic resistancepattern in a microorganism using a second programmable nuclease. 17. Amethod comprising: obtaining a serum sample from a subject; andidentifying a disease status of the subject. 18. A method ofquantification for a disease panel, comprising: assaying for a pluralityof unique target nucleic acids in a plurality of aliquots from a sample,assaying for a control nucleic acid control in a second aliquot of thesample, and quantifying a plurality of signals of the plurality ofunique target nucleic acids by measuring signals produced by cleavage ofdetector nucleic acids compared to the signal produced in the secondaliquot. 19. A method for detecting a target nucleic acid comprising:contacting a target nucleic acid to a pool of guide nucleic acids and aprogrammable nuclease, wherein a guide nucleic acid of the pool of guidenucleic acids has a sequence selected from a group of tiled guidenucleic acid that correspond to nucleic acid of a target nucleic acid;and assaying for a signal produce by cleavage of at least some detectornucleic acids of a population of detector nucleic acids. 20. The system,kit, method, or support medium of any one of embodiments 1-6, whereinthe support medium comprises a lateral flow assay device. 21. Thesystem, kit, method, or support medium of any one of embodiments 1-6,wherein the support medium comprises nitrocellulose. 22. The system,kit, method, or support medium of any one of embodiments 1-6, whereinthe support medium comprises cellulose. 23. The system, kit, method, orsupport medium of any one of embodiments 1-6, wherein the support mediumis a PCR plate or a PCR subset plate. 24. The system, kit, method, orsupport medium of embodiment 23, wherein the PCR plate has 96 wells or384 wells. 25. The system, kit, method, or support medium of embodiment23, wherein the PCR plate or PCR subset plate is paired with afluorescent light reader, a visible light reader, or a mobile device.26. The system, kit, method, or support medium of embodiment 5, whereinthe support medium comprises a sample pad region, a conjugate padregion, a detection region, and an absorbent pad region. 27. The system,kit, method, or support medium of embodiment 26, wherein the conjugatepad region comprises a conjugate, wherein the conjugate comprises ananoparticle, a gold nanoparticle, a latex nanoparticle, or a quantumdot. 28. The system, kit, method, or support medium of embodiment 26,wherein the conjugate comprises a conjugate binding molecule attached toa surface of the conjugate. 29. The system, kit, method, or supportmedium of any one of embodiments 1-6, wherein the detection moietycomprises a fluorescent dye. 30. The system, kit, method, or supportmedium of any one of claims 1-6, wherein the detection moiety comprisesa fluorescence resonance energy transfer (FRET) pair. 31. The system,kit, method, or support medium of any one of embodiments 1-6, whereinthe detection moiety comprises a polypeptide. 32. The system, kit,method, or support medium of any one of embodiments 1-6, wherein thedetection moiety comprises a biotin. 33. The system, kit, method, orsupport medium of any one of embodiments 1-6, wherein the detectionmoiety comprises a polysaccharide, a polymer, or a nanoparticle. 34. Thesystem, kit, method, or support medium of embodiment 28, wherein theconjugate binding molecule binds the detection moiety. 35. The system,kit, method, or support medium of embodiment 34, wherein the conjugatebinding molecule binds selectively to the detection moiety cleaved fromthe detector nucleic acid. 36. The system, kit, method, or supportmedium of embodiment 28, wherein the conjugate binding moleculecomprises an antibody or a fragment of an antibody. 37. The system, kit,method, or support medium of embodiment 28, wherein the conjugatebinding molecule comprises avidin or a polypeptide that binds biotin.38. The system, kit, method, or support medium of embodiment 28, whereinthe conjugate binding molecule comprises a detector moiety bindingnucleic acid. 39. The system, kit, method, or support medium ofembodiment 26, wherein the detection region comprises a capturemolecule, wherein the capture molecule is capable of binding to thedetection moiety, and a control capture molecule. 40. The system, kit,method, or support medium of embodiment 39, wherein the control capturemolecule is capable of binding to a molecule in the sample, detectionmoiety on an uncleaved detection nucleic acid, or a molecule from theconjugate pad region. 41. The system, kit, method, or support medium ofembodiment 39, wherein the capture molecule and the control capturemolecule are located in spatially distinct regions on the detectionregion. 42. The system, kit, method, or support medium of embodiment 39,wherein the capture molecule binds the detection moiety. 43. The system,kit, method, or support medium of embodiment 42, wherein the capturemolecule comprises an antibody or a fragment of an antibody. 44. Thesystem, kit, method, or support medium of embodiment 42, wherein thefirst detection signal is generated by binding of the detection moietyto the capture molecule in the detection region, wherein the firstdetection signal indicates that the sample contained the target nucleicacid. 45. The system, kit, method, or support medium of any one ofembodiments 1-6, wherein the system is capable of detecting more thanone type of target nucleic acid, wherein the system comprises more thanone type of guide nucleic acid and more than one type of detectornucleic acid. 46. The system, kit, method, or support medium of any oneof embodiments 1-6, wherein the detection of the detectable signal bythe support medium increases with cleaving of the detector nucleic acid.47. The system, kit, method, or support medium of any one of embodiments1-6, wherein the detection of the detectable signal by the supportmedium decrease with cleaving of the detector nucleic acid. 48. Thesystem, kit, method, or support medium of any one of embodiments 1-6,wherein the detectable signal is generated directly by the cleavageevent. 49. The system, kit, method, or support medium of any one ofembodiments 1-6, wherein the detectable signal is generated indirectlyby the signal event. 50. The system, kit, method, or support medium ofany one of embodiments 1-6, wherein a second target nucleic acid isdetected on the same support medium. 51. The system, kit, method, orsupport medium of embodiment 50, wherein the second target nucleic acidis targeted by a second guide nucleic acid. 52. The system, kit, method,or support medium of embodiment 37, wherein second target nucleic acidis targeted by a second programmable nucleic acid. 53. The system, kit,method, or support medium of embodiment 50, wherein activation ofnuclease upon complexing with the second target nucleic acid generates asecond detectable signal from a second detection nucleic acid comprisinga second detection moiety. 54. The system, kit, method, or supportmedium of embodiment 53, wherein the second detectable signal isdifferent from the first detectable signal. 55. The system, kit, method,or support medium of embodiment 50, wherein the second target nucleicacid is a related serotype or variant of the first target nucleic acid.56. The system, kit, method, or support medium of embodiment 50, whereinthe system allows multiplexing and detection of multiple target nucleicacids on a single support medium. 57. The system, kit, method, orsupport medium of embodiment 56, wherein there is a guide nucleic acidspecific for each of the multiple target nucleic acids. 58. The system,kit, method, or support medium of embodiment 56, wherein a conjugate padof the support medium comprises a conjugate with a first and a secondconjugate binding molecules attached to a surface of the conjugate,wherein the first and the second conjugate binding molecules bind to thea first and a second detection moieties, respectively. 59. The system,kit, method, or support medium of embodiment 56, wherein a conjugate padof the support medium comprises a first conjugate with a first conjugatebinding molecule, and a second conjugate with a second conjugate bindingmolecule, wherein the first and the second conjugate binding moleculesbind to the a first and a second detection moieties, respectively. 60.The system, kit, method, or support medium of embodiments 58 or 59,wherein the conjugate comprises a nanoparticle, a gold nanoparticle, alatex nanoparticle, or a quantum dot. 61. The system, kit, method, orsupport medium of embodiment 60, wherein a detection region of thesupport medium comprises spatially distinct regions for a first capturemolecule and a second capture molecule, wherein the first and secondcapture molecules bind to first and a second detection moieties,respectively. 62. The system, kit, method, or support medium ofembodiment 60, wherein the second detectable signal is generated in aspatially distinct location than the first generated signal. 63. Thesystem, kit, method, or support medium of embodiment 60, wherein thedetected target nucleic acid is identified based on its spatial locationon the detection region of the support medium. 64. The system, kit,method, or support medium of embodiment 60, wherein a detection regionof the support medium comprises a spatially identical region for a firstcapture molecule and a second capture molecule, wherein the first andsecond capture molecules bind to first and a second detection moieties,respectively. 65. The system, kit, method, or support medium of any oneof embodiments 1-6, wherein the detectable signal is not a fluorescentsignal. 66. The system, kit, method, or support medium of any one ofembodiments 1-6, wherein the detectable signal is a colorimetric orcolor-based signal. 67. The system, kit, method, or support medium ofany one of embodiments 1-6, wherein the support medium comprises abarcode. 68. The system, kit, method, or support medium of embodiment67, wherein the barcode can be scanned using a camera with a mobileapplication. 69. The system, kit, method, or support medium of any oneof embodiments 1-6, wherein the support medium comprises a referencecolor guide. 70. The system, kit, method, or support medium ofembodiment 69, wherein the reference color guide can be scanned using acamera with a mobile application. 71. The system, kit, method, orsupport medium of any one of embodiments 1-6, wherein the target nucleicacid is amplified prior to contacting it to the support medium. 72. Thesystem, kit, method, or support medium of claim 71, wherein theamplification is isothermal amplification. 73. The system, kit, method,or support medium of embodiment 72, wherein the amplification comprisesisothermal recombinase polymerase amplification (RPA), transcriptionmediated amplification (TMA), strand displacement amplification (SDA),helicase dependent amplification (HDA), loop mediated amplification(LAMP), rolling circle amplification (RCA), single primer isothermalamplification (SPIA), ligase chain reaction (LCR), simple methodamplifying RNA targets (SMART), or improved multiple displacementamplification (IMDA). 74. The system, kit, method, or support medium ofany one of embodiments 1-6, wherein the sample is transferred onto thesupport medium. 75. The system, kit, method, or support medium ofembodiment 74, wherein the transfer occurs automatically orsemi-automatically in situ. 76. The system, kit, method, or supportmedium of any one of embodiments 1-6, wherein the support medium isplaced into a reagent chamber holding the sample. 77. The system, kit,method, or support medium of any one of embodiments 1-6, wherein thetarget nucleic acid is not amplified prior to contacting the supportmedium. 78. The system, kit, method, or support medium of any one ofembodiments 1-6, wherein the programmable nuclease is Cas13. 79. Thesystem, kit, method, or support medium of embodiment 78, wherein Cas13is Cas13a, Cas13b, Cas13c, Cas13d, or Cas13e. 80. The system, kit,method, or support medium of any one of embodiments 1-6, wherein theprogrammable nuclease is Cas12. 81. The system, kit, method, or supportmedium of embodiment 80, wherein the Cas12 is Cas12a, Cas12b, Cas12c,Cas12d, or Cas12e. 82. The system, kit, method, or support medium of anyone of embodiments 1-6, wherein the programmable nuclease is Csm1, Cas9,C2c4, C2c8, C2c5, C2c10, C2c9, or casZ. 83. The system, kit, method, orsupport medium of any one of embodiments 1-6, wherein the guide nucleicacid targeting a target sequence is selected from a group of tiled guidenucleic acids that bind to a nucleic acid of a strain of an infection.84. The system, kit, method, or support medium of any one of embodiments1-6, wherein the guide nucleic acid targeting a target sequence isselected from a group of tiled guide nucleic acids that bind to anucleic acid of a strain of HPV 16 or HPV18. 85. The system, kit,method, or support medium of any one of embodiments 1-6, wherein thesample comprises a blood sample, a serum sample, a plasma sample, asaliva sample, a urine sample, a sputum sample, a mucosal sample, aperitoneal fluid sample, a tissue sample, an exudate, an effusion, or acell free DNA sample. 86. The system, kit, method, or support medium ofany one of embodiments 1-6, wherein the sample comprises a non-humananimal sample. 87. The system, kit, method, or support medium of any oneof embodiments 1-6, wherein the sample comprises a plant sample, afungal sample, a bacterial sample, or a viral sample. 88. The system,kit, method, or support medium of any one of embodiments 1-6, whereinthe sample comprises a soil sample, or an environmental sample. 89. Thesystem, kit, method, or support medium of any one of embodiments 1-6,wherein the guide nucleic acid comprises a nucleic acid capable ofdetecting HIV, HPV, chlamydia, gonorrhea, syphilis, trichomoniasis,sexually transmitted infection, malaria, Dengue fever, ebola,chikungunya, leishmaniasis, or combinations thereof. 90. The system,kit, method, or support medium of any one of embodiments 1-6, whereinthe sample comprises a human sample. 91. The system, kit, method, orsupport medium of any one of embodiments 1-6, wherein the guide nucleicacid comprises a nucleic acid capable of detecting a gene. 92. Thesystem, kit, method, or support medium of embodiment 91, wherein thegene is expressed or over expressed in a cancer or is expressed in agenetic disorder. 93. The system, kit, method, or support medium of anyone of embodiments 1-6, wherein the single stranded detector nucleicacid comprises: 1) a nucleic acid comprising at least two nucleotides,2) a fluorophore, and 3) a fluorescence quencher, wherein thefluorophore and the fluorescence quencher are linked by the nucleicacid. 94. The system, kit, method, or support medium of any one ofembodiments 1-6, wherein the single stranded detector nucleic acidcomprises: 1) a nucleic acid comprising at least 3 unmodifiednucleotides, wherein at least two nucleotides are unmodifiedribonucleotides and at least one nucleotide is an unmodifieddeoxyribonucleotide; 2) a fluorophore, and 3) a fluorescence quencher,wherein the fluorophore and the fluorescence quencher are linked by thenucleic acid. 95. The system, kit, method, or support medium of any oneof embodiments 1-6, wherein the single stranded detector nucleic acidcomprises: 1) a nucleic acid comprising at least 3 unmodifiednucleotides, wherein at least two unmodified nucleotides are unmodifieduracil ribonucleotides and at least one nucleotide is an unmodifieddeoxyribonucleotide; 2) a fluorophore, and 3) a fluorescence quencher,wherein the fluorophore and the fluorescence quencher are linked by thenucleic acid. 96. The system, kit, method, or support medium ofembodiment 93, wherein the at least two nucleotides are at least twouracil ribonucleotides. 97. The system, kit, method, or support mediumof embodiment 93, wherein the fluorophore is an infrared fluorescentmoiety. 98. The system, kit, method, or support medium of embodiment 93,wherein the nucleic acid comprises 5 nucleotides, 8 nucleotides, or 10nucleotides. 99. The system, kit, method, or support medium ofembodiment 93, wherein the fluorophore is 5′ 6-FAM and the fluorescencequencher or non-fluorescent fluorescence quencher is 3′ IABkFQ. 100. Thesystem, kit, method, or support medium of embodiment 93, wherein thefluorophore is 5′ 5IRD700 and the fluorescence quencher ornon-fluorescent fluorescence quencher is 3′ IRQC1N. 101. The system,kit, method, or support medium of any one of embodiments 1-6, whereinthe single stranded detector nucleic acid comprises any one of SEQ IDNO: 1—SEQ ID NO: 8. 102. The system or kit of any one of embodiments1-3, further comprising a biological sample. 103. The system or kit ofany one of embodiments 1-3, further comprising a urine sample. 104. Themethod of embodiment 6, wherein the change in color is colorimetricsignal or a signal visible by eye. 105. The method of embodiment 6,wherein cleaving the single stranded detector nucleic acid using theprogrammable nuclease that cleaves with an efficiency of 50% as measuredby a change in color. 106. The method of embodiment 6, wherein the firstdetectable signal is detectable within 60 minutes of the contacting.107. The system, kit, method, or support medium of any one ofembodiments 1-6, wherein the single stranded detector nucleic acid is atleast one population of the single stranded detector nucleic acid. 108.The system, kit, method, or support medium of any one of embodiments1-6, wherein the single stranded detector nucleic acid is any singlestranded detector nucleic acid of Table 4. 109. The system, kit, method,or support medium of any one of embodiments 1-6, wherein the targetsequence comprises a single nucleotide polymorphism. 110. The system,kit, method, or support medium of embodiment 109, wherein the singlenucleotide polymorphism confers resistance to a treatment. 111. Thesystem, kit, method, or support medium of embodiment 110, wherein thetreatment is an antibiotic treatment. 112. A method for detecting atarget nucleic acid, said system comprising: a) providing a sample froma subject; b) introducing the sample into a fluidic device; c)incubating the sample with a pre-complexed programmable nuclease mixturein the fluidic system in an incubation and detection chamber; and d)generating a detection signal in the fluidic system. 113. The method ofembodiment 112, wherein prior to step c), the sample is amplified byincubation with amplification mix. 114. The method of embodiment 112,wherein prior to step b), the sample is filtered using a filtrationdevice for sample preparation. 115. The method of embodiment 114,wherein the filtration device comprises a narrow tip or glass capillaryfor collection of the sample. 116. The method of embodiment 115, whereinthe filtration device comprises a channel to carry the sample. 117. Themethod of embodiment 116, wherein the channel comprises lysis buffer.118. The method of embodiment 116, wherein the channel comprises metal,plastic, or a biocompatible material. 119. The method of embodiment 114,wherein the filtration device further comprises a solution of reagentsthat will lyse a cell. 120. The method of embodiment 119, wherein thesolution comprises chaotropic agents, detergents, salts, or anycombination thereof. 121. The method of embodiment 119, wherein thesolution comprises high osmolality, ionic strength pH, or anycombination thereof. 122. The method of embodiment 119, wherein thesolution comprises a detergent. 123. The method of embodiment 122,wherein the detergent comprises sodium dodecyl sulphate (SDS) or cetyltrimethylammonium bromide (CTAB). 124. The method of embodiment 112,wherein the fluidic device is manufactured from a plastic polymers,poly-methacrylate (PMMA), cyclic olefin polymer (COP), cyclic olefincopolymer (COC), polyethylene (PE), high-density polyethylene (HDPE),polypropylene (PP), glass, silicon, or any combination thereof. 125. Themethod of embodiment 112, wherein features of the fluidic device orembossed using injection molding, (2) micro-milled or micro-engravedusing computer numerical control (CNC) micromachining, or non-contactlaser drilling (by means of a C02 laser source); (3) incorporated viaadditive manufacturing, and/or (4) incorporated via photolithographicmethods. 126. The method of embodiment 112, wherein the fluidic devicecomprises at least three pumps. 127. The method of embodiment 112,wherein the fluidic device comprises at least three reservoirs. 128. Themethod of embodiment 112, wherein the fluidic device comprises up tofour microvalves. 129. The method of embodiment 113, whereinamplification comprises loop-mediated isothermal amplification (LAMP),strand displacement amplification (SDA), recombinase polymeraseamplification (RPA), helicase dependent amplification (HDA), multipledisplacement amplification (MDA), rolling circle amplification (RCA),nucleic acid sequence-based amplification (NASBA), or polymerase chainreaction (PCR). 130. The method of embodiment 128, wherein themicrovalves comprise electro-kinetic microvalves, pneumatic microvalves,vacuum microvalves, capillary microvalves, pinch microvalves,phase-change microvalves, or burst microvalves. 131. The method ofembodiment 112, wherein after step c), sample, amplification mix, andpre-complexed programmable nuclease mix are mixed in a serpentinechannel and led to a chamber. 132. The method of embodiment 131, whereinthe chamber is thermoregulated. 133. The method of embodiment 112,wherein the detection signal is generated by a single stranded detectornucleic acid comprising a detection moiety, wherein the detector nucleicacid is capable of being cleaved by an activated nuclease, therebygenerating the detectable signal. 134. The method of embodiment 133,wherein the detection signal is detected by fluorescence,electrochemical detection, or electrochemiluminescence. 135. The methodof embodiment 112, wherein a fluorimeter is position directly above theincubation and detection chamber. 136. The method of embodiment 112,wherein the top surface of the incubation and detection chamber isfunctionalized with nucleic acid molecules conjugated with a biotinmoiety. 137. The method of embodiment 112, wherein the bottom surface ofthe incubation and detection chamber operates as an electrode and iscoated with streptavidin molecules. 138. The method of any one ofembodiments 136-137, wherein the pre-complexed programmable nuclease mixwith an amplified target nucleic acid flows into the incubation anddetection chamber, is activated at a higher temperature, and cleaves thenucleic acid molecules conjugated with the biotin moiety. 139. Themethod of embodiment 138, wherein the cleaved biotin diffuses to thebottom surface and binds streptavidin, resulting in an increase incurrent. 140. The method of embodiment 112, wherein an electroactivemediator moiety conjugated to individual nucleotides of nucleic acidmolecules (ssRNA, ssDNA or ssRNA/DNA hybrid molecules) are immobilizedon the bottom surface of the incubation and detection chamber. 141. Themethod of embodiment 140, wherein the electroactive mediator moiety isferrocene (Fc). 142. The method of embodiment 140, wherein thepre-complexed programmable nuclease mix with an amplified target nucleicacid flows into the incubation and detection chamber, is activated at ahigher temperature, and cleaves immobilized Fc-conjugated nucleic acidmolecules, resulting in a decrease in current. 143. The method ofembodiment 112, wherein the incubation and detection chambers areseparate. 144. The method of embodiment 143, wherein a top surface ofthe incubation chamber is coated with ssNA conjugated to invertase. 145.The method of embodiment 143, wherein a bottom surface of the incubationchamber comprises a thin-film planar heater. 146. The method ofembodiment 143, wherein a top surface of the detection chamber comprisesa camera or optical sensor. 147. The method of embodiment 143, wherein abottom surface of the detection chamber comprises a thin-film planarheater. 148. The method of embodiment 145, wherein detection comprisesoptical readout using DNS or electrochemical readout with anelectrochemical analyzer or glucometer. 149. The method of embodiment144, wherein the pre-Complexed programmable nuclease mix with anamplified target nucleic acid flows into the incubation and detectionchamber, is activated, and catalyzes breakdown of sucrose to fructoseand glucose. 150. The method of embodiment 149, wherein the amount offructose and glucose is linked to a colorimetric reaction. 151. Themethod of embodiment 149, wherein the pre-Complexed programmablenuclease mix with an amplified target nucleic acid, and glucose flowsinto a separate chamber wherein the separate chamber comprises glucoseoxidase dried on its surface and catalyzes the oxidation of glucose tohydrogen peroxide and D-glucono-δ-lactone. 152. A system for detecting atarget nucleic acid by a programmable nuclease reaction, said systemcomprising a fluidic device, wherein the fluidic device comprises anincubation and detection chamber. 153. The system of embodiment 152,wherein features of the fluidic device or embossed using injectionmolding, (2) micro-milled or micro-engraved using computer numericalcontrol (CNC) micromachining, or non-contact laser drilling (by means ofa C02 laser source); (3) incorporated via additive manufacturing, and/or(4) incorporated via photolithographic methods. 154. The system ofembodiment 152, wherein the fluidic device comprises at least threepumps. 155. The system of embodiment 152, wherein the fluidic devicecomprises at least three reservoirs. 156. The system of embodiment 152,wherein the fluidic device comprises up to four microvalves. 157. Thesystem of embodiment 156, wherein the microvalves compriseelectro-kinetic microvalves, pneumatic microvalves, vacuum microvalves,capillary microvalves, pinch microvalves, phase-change microvalves, orburst microvalves. 158. The system of embodiment 152, wherein the topsurface of the incubation and detection chamber is functionalized withnucleic acid molecules conjugated with a biotin moiety. 159. The systemof embodiment 152, wherein the bottom surface of the incubation anddetection chamber operates as an electrode and is coated withstreptavidin molecules. 160. The system of embodiment 152, wherein anelectroactive mediator moiety conjugated to individual nucleotides ofnucleic acid molecules (ssRNA, ssDNA or ssRNA/DNA hybrid molecules) areimmobilized on the bottom surface of the incubation and detectionchamber. 161. The system of embodiment 160, wherein the electroactivemediator moiety is ferrocene (Fc). 162. The system of embodiment 152,wherein the incubation and detection chambers are separate. 163. Thesystem of embodiment 162, wherein a top surface of the incubationchamber is coated with ssDNA conjugated to invertase. 164. The system ofembodiment 162, wherein a bottom surface of the incubation chambercomprises a thin-film planar heater. 165. The system of embodiment 162,wherein a top surface of the detection chamber comprises a camera oroptical sensor. 166. The system of embodiment 162, wherein a bottomsurface of the detection chamber comprises a thin-film planar heater.167. The system of embodiment 162, wherein the fluidic device comprisesa separate chamber comprising glucose oxidase dried on its surface. 168.The method of any one of embodiments 112-151, wherein the pre-complexedprogrammable nuclease mixture comprises a guide RNA complementary to thetarget nucleic acid and a Cas nuclease. 169. The method of embodiment12, wherein the first programmable nuclease is an RNase. 170. The methodof embodiment 12, wherein the first programmable nuclease is a DNase.171. The method of embodiment 12, wherein the second programmablenuclease is a DNase. 172. The method of embodiment 12, wherein thesecond programmable nuclease is a RNase. 173. The method of embodiment12, wherein the first programmable nuclease is Cas protein. 174. Themethod of embodiment 12, wherein the second programmable nuclease is aCas protein. 175. The method of embodiment 12, wherein the firstprogrammable nuclease is Cas13. 176. The method of embodiment 12,wherein the second programmable nuclease is Cas12. 177. The method ofembodiment 12, wherein the second programmable nuclease is Cas14. 178.The method of embodiment 12, wherein the assaying for the pathogenicnucleic acid in the sample and the pathogen resistance locus in thesample are performed in a common reaction volume. 179. The method ofembodiment 12, wherein the pathogen resistance locus is a host locusthat confers host resistance to the pathogen. 180. The method ofembodiment 12, wherein the pathogen resistance locus is a pathogen locusthat confers resistance to disease treatment. 181. The method ofembodiment 12, wherein the pathogen resistance locus is a pathogen locusthat confers resistance to antibiotic treatment. 182. The method ofembodiment 12, wherein cleavage of a first detector nucleic acid uponactivation of the first programmable nuclease indicates a presence of aspecies of pathogen, and cleavage of a second detector nucleic acid uponactivation of the second programmable nuclease indicates a presence ofan antibiotic resistant SNP of the species of pathogen. 183. The methodof embodiment 13, wherein the first programmable nuclease is an RNase.184. The method of claim 13, wherein the first programmable nuclease isa DNase. 185. The method of embodiment 13, wherein the secondprogrammable nuclease is a DNase. 186. The method of embodiment 13,wherein the second programmable nuclease is a RNase. 187. The method ofembodiment 13, wherein the first programmable nuclease is Cas protein.188. The method of embodiment 13, wherein the second programmablenuclease is a Cas protein. 189. The method of embodiment 13, wherein thefirst programmable nuclease is Cas13. 190. The method of embodiment 13,wherein the second programmable nuclease is Cas12. 191. The method ofembodiment 13, wherein the second programmable nuclease is Cas14. 192.The method of embodiment 13, wherein the assaying for the pathogenicnucleic acid in the sample and the pathogen resistance locus in thesample are performed in a common reaction volume. 193. The system ofembodiment 7 further comprising at least one additional guide nucleicacid selected from a group of tiled guide nucleic acid that correspondto nucleic acid of a strain of an infectious agent and wherein the guidenucleic acid and the at least one additional guide nucleic acid comprisedifferent sequences. 194. The method of embodiment 10, wherein thedetected signal is generated in no more than 15 minutes. 195. The methodof embodiment 10, wherein the detected signal is generated in no morethan 10 minutes. 196. The method of embodiment 10, wherein the detectedsignal is generated in no more than 5 minutes. 197. The method ofembodiment 10, wherein the target nucleic acid is amplified before thecontacting. 198. The method of embodiment 197, wherein the amplificationis isothermal amplification. 199. The method of embodiment 10, whereinthe sample is urine. 200. The method of embodiment 10, wherein thesample is saliva. 201. The method of embodiment 10, wherein the sampleis blood. 202. The method of embodiment 14, wherein the output comprisesfluorescence/second. 203. The method of embodiment 14, wherein thereaction rate log linear for output signal and target nucleic acidconcentration. 204. The method of embodiment 14, wherein the signaloutput is correlated with the target nucleic acid concentration. 205.The method of embodiment 14, wherein the target nucleic acid is RNA.206. The method of embodiment 14, wherein the target nucleic acid isDNA. 207. The method of embodiment 15, wherein a total time for nucleicacid detection is no greater than 60 minutes. 208. The method ofembodiment 15, wherein a total time for nucleic acid detection is nogreat than 50 minutes. 209. The method of embodiment 15, wherein a totaltime for nucleic acid detection is no greater than 40 minutes. 210. Themethod of embodiment 15, wherein a total time for nucleic acid detectionis no greater than 30 minutes. 211. The method of embodiment 15, whereinthe sample is obtained from a swab. 212. The method of embodiment 15,wherein the sample is obtained from urine. 213. The method of embodiment15, wherein the sample is obtained from blood. 214. The method ofembodiment 15, wherein the sample is contained in no more than 20 μl.215. The method of embodiment 16, wherein the first programmablenuclease and the second programmable nuclease do not cleave a commondetector nucleic acid site upon activation. 216. The method ofembodiment 17, wherein the disease status is cancer status. 217. Themethod of embodiment 17, wherein the disease status is prostate cancerstatus. 218. The method of embodiment 18, wherein the plurality ofunique target nucleic acids are from a plurality of bacterial pathogensin the sample. 219. The method of embodiment 18, wherein thequantification of a signal of the plurality correlates with aconcentration of a unique target nucleic acid of the plurality for theunique target nucleic acid of the plurality that produced the signal ofthe plurality. 220. The method of embodiment 19, wherein the tiled guidenucleic acids are sequentially tiled. 221. The method of embodiment 19,wherein the tiled guide nucleic acids have overlapping tiling. 222. Themethod of embodiment 19, wherein the tiled guide nucleic acids arenon-sequentially tiled. 223. The system, kit, method, or support mediumof any one of embodiments 1-222, further comprising a reporter. 224. Thesystem, kit, method, or support medium of embodiment 223, wherein thereporter comprises a biotin. 225. The system, kit, method, or supportmedium of any one of embodiments 223-224, wherein the reporter comprisesa methylene blue molecule. 226. The system, kit, method, or supportmedium of any one of embodiments 223-225, wherein cleavage of thereporter by a Cas protein results in an increase in current. 227. Thesystem, kit, method, or support medium of any one of embodiments223-226, wherein the reporter comprises a nucleic acid linker conjugatedto biotin-dT at the 5′ end, a FAM reporter at the 5′ end, or acombination thereof. 228. The system, kit, method, or support medium ofany one of embodiments 223-227, wherein the reporter is conjugated to asubstrate at the 3′ end. 229. The system, kit, method, or support mediumof embodiment 228, wherein the substrate comprises a reaction chamber.230. The system, kit, method, or support medium of any one ofembodiments 228-229, wherein the substrate comprises a bead. 231. Thesystem, kit, method, or support medium of any one of embodiments223-230, wherein the bead is a magnetic bead. 232. The system, kit,method, or support medium of any one of embodiments 223-231, wherein asignal is visualized by a nanoparticle. 233. The system, kit, method, orsupport medium of embodiment 232, wherein the nanoparticle comprises agold nanoparticle. 234. The system, kit, method, or support medium ofany one of embodiments 223-233, wherein the reporter is cleaved by a Casprotein in a reaction chamber upstream of a test strip to generate acleaved reporter. 235. The system, kit, method, or support medium of anyone of embodiments 223-234, wherein the test strip comprises astreptavidin at a first test line spaced downstream of the reactionchamber. 236. The system, kit, method, or support medium of embodiment235, wherein the streptavidin binds the cleaved reporter. 237. Thesystem, kit, method, or support medium of any one of embodiments233-236, wherein the gold nanoparticle is coated with an anti-reporterantibody. 238. The system, kit, method, or support medium of embodiment237, wherein the anti-reporter antibody coated gold nanoparticle bindsto the cleaved reporter at the test line. 239. The system, kit, method,or support medium of any one of embodiments 223-238, wherein a flowcontrol line is spaced downstream of the test line. 240. The system,kit, method, or support medium of any one of embodiments 223-239,wherein the flow control line comprises a control antibody, which bindsthe anti-reporter antibody conjugated gold nanoparticles. 241. A methodof assaying for a target nucleic acid in a sample, comprising: a)contacting the sample to a complex comprising a guide nucleic acidcomprising a segment that is reverse complementary to a segment of thetarget nucleic acid and a programmable nuclease that exhibits sequenceindependent cleavage upon forming a complex comprising the segment ofthe guide nucleic acid binding to the segment of the target nucleicacid; and b) assaying for a signal indicating cleavage of at least someprotein-nucleic acids of a population of protein-nucleic acids, whereinthe signal indicates a presence of the target nucleic acid in the sampleand wherein absence of the signal indicates an absence of the targetnucleic acid in the sample. 242. The method of embodiment 241, wherein aprotein-nucleic acid of the population of protein nucleic acids is anenzyme-nucleic acid. 243. The method of embodiment 241, wherein aprotein-nucleic acid of the population of protein nucleic acids is anenzyme substrate-nucleic acid. 244. The method of embodiment 242,wherein an enzyme of the enzyme-nucleic acid is an invertase enzyme.245. The method of embodiment 242, wherein an enzyme of theenzyme-nucleic acid is a sterically hindered enzyme. 246. The method ofembodiment 245, wherein upon cleavage of a nucleic acid of theenzyme-nucleic acid, the enzyme is functional. 247. The method ofembodiment 241, wherein the population of protein-nucleic acids isattached to a solid support. 248. The method of embodiment 247, whereinthe solid support is a surface. 249. The method of embodiment 248,wherein the surface is an electrode. 250. The method of embodiment 247,wherein the solid support is a bead. 251. The method of embodiment 250,wherein the bead is a magnetic bead. 252. The method of embodiment 241,wherein the signal is a calorimetric signal. 253. The method ofembodiment 252, wherein the calorimetric signal is heat produced afterthe cleavage of the at least some protein-nucleic acids. 254. The methodof embodiment 252, wherein the calorimetric signal is heat absorbedafter the cleavage of the at least some protein-nucleic acids. 255. Themethod of embodiment 241, wherein the signal is a potentiometric signal.256. The method of embodiment 255, wherein the potentiometric signal iselectric potential produced after the cleavage of the at least someprotein-nucleic acids. 257. The method of embodiment 241, wherein thesignal is an amperometric signal. 258. The method of embodiment 257,wherein the amperometric signal is movement of electrons produced afterthe cleavage of the at least some protein-nucleic acids. 259. The methodof embodiment 241, wherein the signal is an optical signal. 260. Themethod of embodiment 259, wherein the optical signal is a colorometricsignal. 261. The method of embodiment 259, wherein the optical signal isa fluorescence signal. 262. The method of embodiment 259, wherein theoptical signal is a light output produced after the cleavage of the atleast some protein-nucleic acids. 263. The method of embodiment 259,wherein the optical signal is a change in light absorbance betweenbefore and after the cleavage of the at least some protein-nucleicacids. 264. The method of embodiment 241, wherein the signal is apiezo-electric signal. 265. The method of embodiment 264, wherein thepiezo-electric signal is a change in mass between before and after thecleavage of the at least some protein-nucleic acids. 266. The method ofembodiment 241 further comprising contacting a mixture produced by stepa) to an enzyme substrate of a protein of the population ofprotein-nucleic acids. 267. The method of embodiment 266, wherein theenzyme substrate comprises sucrose and DNS reagent. 268. The method ofembodiment 241, wherein a nucleic acid of the population ofprotein-nucleic acids is single stranded DNA. 269. The method ofembodiment 241, wherein a nucleic acid of the population ofprotein-nucleic acids is single stranded RNA. 270. The method ofembodiment 241, wherein a nucleic acid of the population ofprotein-nucleic acids is a single stranded DNA/RNA hybrid. 271. Themethod of embodiment 241, further comprising the amplifying the targetnucleic acid before step a). 272. The method of embodiment 271, whereinthe amplifying comprises thermal cycling amplification. 273. The system,kit, method, or support medium of embodiment 30, wherein the amplifyingcomprises isothermal amplification. 274. The system, kit, method, orsupport medium of embodiment 273, wherein the isothermal amplificationis select from the group consisting of isothermal recombinase polymeraseamplification (RPA), transcription mediated amplification (TMA), stranddisplacement amplification (SDA), helicase dependent amplification(HDA), loop mediated amplification (LAMP), rolling circle amplification(RCA), single primer isothermal amplification (SPIA), ligase chainreaction (LCR), simple method amplifying RNA targets (SMART), improvedmultiple displacement amplification (IMDA), and nucleic acidsequence-based amplification (NASBA). 275. The method of embodiment 241,wherein the programmable nuclease is a target nucleic acid activatedeffector protein that exhibits sequence independent cleavage uponactivation. 276. The method of embodiment 241, wherein the programmablenuclease is an RNA guided nuclease. 277. The method of embodiment 241,wherein the programmable nuclease comprises a Cas nuclease. 278. Themethod of embodiment 277, wherein the Cas nuclease is Cas13. 279. Themethod of embodiment 278, wherein the Cas13 is Cas13a, Cas13b, Cas13c,Cas13d, or Cas13e. 280. The method of embodiment 277, wherein the Casnuclease is Cas12. 281. The method of embodiment 280, wherein the Cas12is Cas12a, Cas12b, Cas12c, Cas12d, or Cas12e. 282. The method ofembodiment 277, wherein the Cas nuclease is Cas14. 283. The method ofembodiment 282, wherein the Cas14 is Cas14a, Cas14b, Cas14c, Cas14d,Cas14e, Cas14f, Cas14g, or Cas14h. 284. The method of embodiment 277,wherein the Cas nuclease is Csm1, Cas9, C2c4, C2c8, C2c5, C2c10, orC2c9. 285. The method of embodiment 241, wherein the guide nucleic acidcomprises a crRNA. 286. The method of embodiment 241, wherein the guidenucleic acid comprises a crRNA and a tracrRNA. 287. The method ofembodiment 241, wherein the signal is present prior to protein-nucleicacid cleavage. 288. The method of embodiment 241, wherein the signal isabsent prior to protein-nucleic acid cleavage. 289. The method ofembodiment 241, wherein the sample comprises blood, serum, plasma,saliva, urine, mucosal sample, peritoneal sample, cerebrospinal fluid,gastric secretions, nasal secretions, sputum, pharyngeal exudates,urethral or vaginal secretions, an exudate, an effusion, or tissue. 290.A method of assaying for a target nucleic acid in a sample, comprising:a) contacting the sample to a complex comprising a guide nucleic acidcomprising a segment that is reverse complementary to a segment of thetarget nucleic acid and a programmable nuclease that exhibits sequenceindependent cleavage upon forming a complex comprising the segment ofthe guide nucleic acid binding to the segment of the target nucleicacid; b) contacting the complex to a substrate; c) contacting thesubstrate to a reagent that differentially reacts with a cleavedsubstrate; and d) assaying for a signal indicating cleavage of thesubstrate, wherein the signal indicates a presence of the target nucleicacid in the sample and wherein absence of the signal indicates anabsence of the target nucleic acid in the sample. 291. The method ofembodiment 290, wherein the substrate is an enzyme-nucleic acid. 292.The method of embodiment 290, wherein the substrate is an enzymesubstrate-nucleic acid. 293. The method of embodiment 291, wherein anenzyme of the enzyme-nucleic acid is an invertase enzyme. 294. Themethod of embodiment 291, wherein an enzyme of the enzyme-nucleic acidis a sterically hindered enzyme. 295. The method of embodiment 294,wherein upon cleavage of a nucleic acid of the enzyme-nucleic acid, theenzyme is functional. 296. The method of embodiment 290, wherein thesubstrate is attached to a solid support. 297. The method of embodiment296, wherein the solid support is a surface. 298. The method ofembodiment 297, wherein the surface is an electrode. 299. The method ofembodiment 296, wherein the solid support is a bead. 300. The method ofembodiment 250, wherein the bead is a magnetic bead. 301. The method ofembodiment 290, wherein the signal is a calorimetric signal. 302. Themethod of embodiment 301, wherein the calorimetric signal is heatproduced after the cleavage of the substrate. 303. The method ofembodiment 301, wherein the calorimetric signal is heat absorbed afterthe cleavage of the substrate. 304. The method of embodiment 290,wherein the signal is a potentiometric signal. 305. The method ofembodiment 304, wherein the potentiometric signal is electric potentialproduced after the cleavage of the substrate. 306. The method ofembodiment 290, wherein the signal is an amperometric signal. 307. Themethod of embodiment 306, wherein the amperometric signal is movement ofelectrons produced after the cleavage of the substrate. 308. The methodof embodiment 290, wherein the signal is an optical signal. 309. Themethod of embodiment 308, wherein the optical signal is a colorometricsignal. 310. The method of embodiment 308, wherein the optical signal isa fluorescence signal. 311. The method of embodiment 308, wherein theoptical signal is a light output produced after the cleavage of thesubstrate. 312. The method of embodiment 308, wherein the optical signalis a change in light absorbance between before and after the cleavage ofthe substrate. 313. The method of embodiment 290, wherein the signal isa piezo-electric signal. 314. The method of embodiment 313, wherein thepiezo-electric signal is a change in mass between before and after thecleavage of the substrate. 315. The method of embodiment 291, whereinthe reagent comprises an enzyme substrate. 316. The method of embodiment292, wherein the reagent comprises an enzyme. 317. The method ofembodiment 315, wherein the enzyme substrate comprises sucrose and DNSreagent. 318. The method of embodiment 290, wherein the reagentcomprises a single stranded DNA. 319. The method of embodiment 290,wherein the reagent comprises a single stranded RNA. 320. The method ofembodiment 290, wherein the reagent comprises a single stranded DNA/RNAhybrid. 321. The method of embodiment 290, further comprising theamplifying the target nucleic acid before step a). 322. The method ofembodiment 321, wherein the amplifying comprises thermal cyclingamplification. 323. The method of embodiment 321, wherein the amplifyingcomprises isothermal amplification. 324. The method of embodiment 323,wherein the isothermal amplification is select from the group consistingof isothermal recombinase polymerase amplification (RPA), transcriptionmediated amplification (TMA), strand displacement amplification (SDA),helicase dependent amplification (HDA), loop mediated amplification(LAMP), rolling circle amplification (RCA), single primer isothermalamplification (SPIA), ligase chain reaction (LCR), simple methodamplifying RNA targets (SMART), improved multiple displacementamplification (IMDA), and nucleic acid sequence-based amplification(NASBA). 325. The method of embodiment 290, wherein the programmablenuclease is a target nucleic acid activated effector protein thatexhibits sequence independent cleavage upon activation. 326. The methodof embodiment 290, wherein the programmable nuclease is an RNA guidednuclease. 327. The method of embodiment 290, wherein the programmablenuclease comprises a Cas nuclease. 328. The method of embodiment 327,wherein the Cas nuclease is Cas13. 329. The method of embodiment 328,wherein the Cas13 is Cas13a, Cas13b, Cas13c, Cas13d, or Cas13e. 330. Themethod of embodiment 327, wherein the Cas nuclease is Cas12. 331. Themethod of embodiment 330, wherein the Cas12 is Cas12a, Cas12b, Cas12c,Cas12d, or Cas12e. 332. The method of embodiment 327, wherein the Casnuclease is Cas14. 333. The method of embodiment 332, wherein the Cas14is Cas14a, Cas14b, Cas14c, Cas14d, Cas14e, Cas14f, Cas14g, or Cas14h.334. The method of embodiment 327, wherein the Cas nuclease is Csm1,Cas9, C2c4, C2c8, C2c5, C2c10, or C2c9. 335. The method of embodiment291, wherein the guide nucleic acid comprises a crRNA. 336. The methodof embodiment 291, wherein the guide nucleic acid comprises a crRNA anda tracrRNA. 337. The method of embodiment 291, wherein the signal ispresent prior to substrate cleavage. 338. The method of embodiment 291,wherein the signal is absent prior to substrate acid cleavage. 339. Themethod of embodiment 291, wherein the sample comprises blood, serum,plasma, saliva, urine, mucosal sample, peritoneal sample, cerebrospinalfluid, gastric secretions, nasal secretions, sputum, pharyngealexudates, urethral or vaginal secretions, an exudate, an effusion, ortissue. 340. The method of embodiment 19, wherein the of guide nucleicacids provides broad spectrum identification of the target nucleic acid.341. The method of embodiment 290, wherein the target nucleic acid isDNA and the programmable nuclease is Cas13. 342. The method ofembodiment 341, wherein the Cas13 is Cas13a. 343. The method ofembodiment 342, wherein the Cas13a is Lbu-Cas13a or Lwa-Cas13a. 344. Themethod of embodiment 340, wherein the target nucleic acid lacks aguanine at the 3′ end. 345. The method of embodiment 341, wherein thesequence independent cleavage occurs from pH 6.8 to pH 8.2. 346. Amethod of assaying for a target DNA sequence in a sample, the methodcomprising: contacting the sample to a complex comprising a guidenucleic acid comprising a segment that is reverse complementary to asegment of the target DNA sequence and a Type VI programmable nuclease;hybridizing the segment of the guide nucleic acid to the segment of thetarget DNA sequence, thereby activating the Type VI programmablenuclease to cleave an RNA sequence via sequence independent cleavage.347. The method of embodiment 346, wherein the method further comprisesgenerating a detectable signal upon the sequence independent cleavage ofthe RNA sequence. 348. The method of embodiment 347, further comprisingassaying for the detectable signal. 349. The method of any one ofembodiments 346-348, wherein the Type VI programmable nuclease is aCas13 programmable nuclease. 350. The method of embodiment 349, whereinthe Cas13 programmable nuclease is a Cas13a programmable nuclease. 351.The method of embodiment 350, wherein the Cas13a programmable nucleasecomprises Lbu-Cas13a or Lwa-Cas13a. 352. The method of any one ofembodiments 346-351, wherein the equence independent cleavage occursfrom pH 6.8 to pH 8.2. 353. The method of any one of embodiments346-351, wherein the target DNA sequence lacks a guanine at the 3′ end.354. The method of any one of embodiments 346-353, wherein the targetDNA sequence is ssDNA. 355. The method of any one of embodiments346-353, wherein the target DNA sequence is present in an organism. 356.The method of embodiment 355, wherein the organism is a virus orbacteria, 357. The method of any one of embodiments 346-353, wherein thetarget DNA sequence is generated by a nucleic acid amplification method.358. The method of embodiment 357, wherein the nucleic acidamplification method comprises recombinase polymerase amplification(RPA), transcription mediated amplification (TMA), strand displacementamplification (SDA), helicase dependent amplification (HDA), loopmediated amplification (LAMP), rolling circle amplification (RCA),single primer isothermal amplification (SPIA), ligase chain reaction(LCR), simple method amplifying RNA targets (SMART), improved multipledisplacement amplification (IMDA), and nucleic acid sequence-basedamplification (NASBA), or PCR. 359. The method of any one of embodiments347-358, wherein the detectable signal is fluorescence, luminescence,colorimetric, electrochemical, enzymatic, calorimetric, optical,amperometric, or potentiometric. 360. The method of any one ofembodiments 346-359, further comprising multiplexing with a complex of asecond guide nucleic acid comprising a second segment that is reversecomplementary to a second segment of a second target DNA sequence and aType V programmable nuclease. 361. The method of embodiment 360, whereinthe Type V programmable nuclease is Cas12. 362. The method of embodiment361, wherein the Cas12 is Cas12 is Cas12a, Cas12b, Cas12c, Cas12d, orCas12e. 363. The method of any one of embodiments 346-362, wherein theguide nucleic acid comprises a crRNA. 364. The method of any one ofembodiments 346-363, wherein the guide nucleic acid comprises a crRNAand a tracrRNA. 365. The method of any one of embodiments 347-364,wherein the detectable signal is present prior to substrate cleavage.366. The method of any one of embodiments 347-364, wherein thedetectable signal is absent prior to substrate acid cleavage. 367. Themethod of any one of embodiments 346-366, wherein the sample comprisesblood, serum, plasma, saliva, urine, mucosal sample, peritoneal sample,cerebrospinal fluid, gastric secretions, nasal secretions, sputum,pharyngeal exudates, urethral or vaginal secretions, an exudate, aneffusion, or tissue. 368. The method of any one of embodiments 346-367,wherein the method is carried out on a support medium. 369. The methodof any one of embodiments 346-368, wherein the method is carried out ona lateral flow assay device.

The following embodiments recite permutations of combinations offeatures disclosed herein. In some cases, permutations of combinationsof features disclosed herein are non-limiting. In other casespermutations of combinations of features disclosed herein are limiting.Other permutations of combinations of features are also contemplated. Inparticular, each of these numbered embodiments is contemplated asdepending from or relating to every previous or subsequent numberedembodiment, independent of their order as listed. 1. A method ofdetecting a target nucleic acid in a sample, the method comprising:contacting a first volume to a second volume, wherein the first volumecomprises the sample and the second volume comprises: a programmablenuclease; a guide nucleic acid having a portion reverse complementary toa portion of a target nucleic acid in the sample; and a reporter,wherein the second volume is at least 4-fold greater than the firstvolume; and detecting the presence or the absence of the target nucleicacid by measuring a signal produced by cleavage of the reporter, whereincleavage occurs when the programmable nuclease is activated. 2. Themethod of any preceding embodiment, wherein the reporter is a hybridnucleic acid reporter. 3. The method of any preceding embodiment,wherein the method further comprises amplifying the target nucleic acid.4. A method of detecting a target nucleic acid in a sample, the methodcomprising: contacting the sample to: a programmable nuclease; a guidenucleic acid having a portion reverse complementary to a portion of thetarget nucleic acid; and a hybrid nucleic acid reporter; and assayingfor a signal generated by cleavage of the hybrid nucleic acid reporter.5. The method of any preceding embodiment, wherein the contactingcomprises contacting a first volume to a second volume, wherein thefirst volume comprises the sample and the second volume comprises theprogrammable nuclease, the guide nucleic acid, and the hybrid nucleicacid reporter and wherein the second volume is at least 4-fold greaterthan the first volume. 6. The method of any preceding embodiment,wherein the method further comprises amplifying the target nucleic acid.7. A method of disease detection, the method comprising: contacting asample to a first programmable nuclease and a first guide nucleic acidhaving a portion reverse complementary to a portion of a first targetnucleic acid from a disease causing organism; and a second programmablenuclease and a second guide nucleic acid having a portion reversecomplementary to a portion of a second target nucleic acid from anantibiotic resistant locus of the disease causing organism; and assayingfor: a first signal generated by cleavage of a first reporter; and asecond signal generated by cleavage of a second reporter. 8. The methodof any preceding embodiment, wherein the disease causing organism isNeisseria gonorrhoeae, Acinetobacter baumannii, Staphylococcus aureus,Burkholderia cepacia, Pseudomonas aeruginosa, Escherichia coli,Mycobacterium tuberculosis, Klebsiella pneumoniae, or Streptococcuspyogenes. 9. The method of any preceding embodiment, wherein theantibiotic resistant locus of the disease causing organism confersresistance to vancomycin, erythromycin, clindamycin, or any combinationthereof. 10. The method of any preceding embodiment, wherein the firstprogrammable nuclease is a Type V programmable nuclease or a Type VIprogrammable nuclease. 11. The method of any preceding embodiment,wherein the second programmable nuclease is a Type V programmablenuclease or a Type VI programmable nuclease. 12. The method of anypreceding embodiment, wherein the Type V programmable nuclease is aCas12 or a Cas14. 13. The method of any preceding embodiment, whereinthe Type VI programmable nuclease is a Cas13. 14. The method of anypreceding embodiment, wherein the Cas12 is Cas12 is Cas12a, Cas12b,Cas12c, Cas12d, or Cas12e. 15. The method of any preceding embodiment,wherein the Cas14 is Cas14a, Cas14b, Cas14c, Cas14d, Cas14e, Cas14f,Cas14g, or Cas14h. 16. The method of any preceding embodiment, whereinthe Cas13 is Cas13a, Cas13b, Cas13c, Cas13d, or Cas13e. 17. The methodof any preceding embodiment, wherein the first reporter, the secondreporter, or a combination thereof comprises a nucleic acid, an affinitymolecule, a detection molecule, a quencher, or any combination thereof.18. The method of any preceding embodiment, wherein the nucleic acid ofthe first reporter and the nucleic acid of the second reporter aredifferent. 19. The method of any preceding embodiment, wherein thedetection molecule of the first reporter and the detection molecule ofthe second reporter are different. 20. The method of any precedingembodiment, wherein the sample is from a subject. 21. The method of anypreceding embodiment, wherein if only the first signal appears, themethod further comprises administering an antibiotic corresponding tothe antibiotic resistant locus to the subject. 22. The method of anypreceding embodiment, wherein if the first signal and second signalappears, the method further comprises treating with an orthogonalantibiotic to the subject. 23. A method of treating a subject, themethod comprising: detecting a presence or an absence of a signal by:contacting a sample containing a target nucleic acid from the subjectto: a programmable nuclease; a guide nucleic acid having a portionreverse complementary to a portion of the target nucleic acid; and areporter; and assaying for the presence of the signal generated bycleavage of the reporter; and treating the subject. 24. The method ofany preceding embodiment, wherein the treating comprises administering atherapy. 25. The method of any preceding embodiment, wherein the therapycomprises radiation, chemotherapy, antibiotics, antivirals, orantifungals. 26. The method of any preceding embodiment, wherein theadministering is parenteral, topical, or local. 27. The method of anypreceding embodiment, wherein the subject has a symptom of a disease.28. The method of any preceding embodiment, wherein the subject isasymptomatic. 29. The method of any preceding embodiment, wherein themethod comprises amplifying the target nucleic acid. 30. The method ofany preceding embodiment, wherein the contacting comprises contacting afirst volume to a second volume, wherein the first volume comprises thesample and the second volume comprises the programmable nuclease, theguide nucleic acid, and the reporter, and wherein the second volume isat least 4-fold greater than the first volume. 31. The method of anypreceding embodiment, wherein the second volume is at least 4-foldgreater to at least 50-fold greater than the first volume. 32. Themethod of any preceding embodiment, wherein the second volume is atleast 10-fold greater than the first volume. 33. The method of anypreceding embodiment, wherein the total nucleic acids includes thetarget nucleic acid and non-target nucleic acids. 34. The method of anypreceding embodiment, wherein the non-target nucleic acids are from thesample. 35. The method of any preceding embodiment, wherein thenon-target nucleic acids are from an amplified sample. 36. The method ofany preceding embodiment, wherein the target nucleic acid comprises theforward primer, the reverse primer, ssDNA generated from amplification,or any combination thereof. 37. The method of any preceding embodiment,wherein the method comprises lysing the sample. 38. The method of anypreceding embodiment, wherein the reporter comprises a nucleic acid, anaffinity molecule, a detection molecule, a quencher, or any combinationthereof. 39. The method of any preceding embodiment, wherein the nucleicacid is conjugated at one end to the affinity molecule and the detectionmolecule. 40. The method of any preceding embodiment, wherein thenucleic acid is a single stranded nucleic acid. 41. The method of anypreceding embodiment, wherein the single stranded nucleic acid is singlestranded DNA. 42. The method of any preceding embodiment, wherein thesingle stranded nucleic acid is single stranded RNA. 43. The method ofany preceding embodiment, wherein the affinity molecule is biotin. 44.The method of any preceding embodiment, wherein the detection moleculeis a fluorescent molecule, an electrochemical molecule, or an enzyme.45. The method of any preceding embodiment, wherein the fluorescentmolecule is 6-fluorescein, IRDye 700, TYE 665, ALEXA FLUOR 594, ATTO TM633, or Iowa Black RQ. 46. The method of any preceding embodiment,wherein the electrochemical molecule comprises biotin, ferrocene,digoxigenin, or invertase. 47. The method of any preceding embodiment,wherein the quencher is IABkFQ or IRQC1N. 48. The method of anypreceding embodiment, wherein the programmable nuclease, the reporter,the guide nucleic acid, the forward primer, the reverse primer, thedeoxynucleotide triphosphate, the reverse transcriptase, the T7promoter, the T7 polymerase, or any combination thereof are lyophilizedor vitrified. 49. The method of any preceding embodiment, wherein theprogrammable nuclease, the reporter, the guide nucleic acid, the forwardprimer, the reverse primer, the deoxynucleotide triphosphate, thereverse transcriptase, the T7 promoter, the T7 polymerase, or anycombination thereof are suspended in a buffer. 50. The method of anypreceding embodiment, wherein the reporter is immobilized to the surfaceof the detection chamber 51. The method of any preceding embodiment,wherein the reporter is present at a concentration of from 10 nM to 1000nM. 52. The method of any preceding embodiment, wherein the reporter ispresent at a concentration of from 100 to 500 nM of reporter. 53. Themethod of any preceding embodiment, wherein the forward primer, thereverse primer, the deoxynucleotide triphosphate, the reversetranscriptase, the T7 promoter, the T7 polymerase, or any combinationthereof are suspended in an amplification buffer. 54. The method of anypreceding embodiment, wherein the method comprises from 1 nM to 100 nMof target nucleic acids. 55. The method of any preceding embodiment,wherein the method comprises from 1 nM to 1000 nM of total nucleicacids. 56. The method of any preceding embodiment, wherein the methodcomprises from 10 to 25 nM of total nucleic acids. 57. The method of anypreceding embodiment, wherein the method comprises a plurality of guideRNAs. 58. The method of any preceding embodiment, wherein the pluralityof guide RNAs have the same sequence. 59. The method of any precedingembodiment, wherein the sequence of at least one guide RNA of theplurality of guide RNAs is unique. 60. The method of any precedingembodiment, wherein at least one guide RNAs of the plurality of guideRNAs has a portion reverse complementary to a portion of a targetnucleic acid different than a second RNA of the plurality of guide RNAs.61. The method of any preceding embodiment, wherein the plurality ofguide RNAs comprise at least 20 guide RNAs. 62. The method of anypreceding embodiment, wherein each of the 20 guide RNAs has a portionreverse complementary to a portion of a different target nucleic acid.63. The method of any preceding embodiment, wherein the sample is abiological sample. 64. The method of any preceding embodiment, whereinthe biological sample is blood, serum, plasma, saliva, urine, mucosalsample, peritoneal sample, cerebrospinal fluid, gastric secretions,nasal secretions, sputum, pharyngeal exudates, urethral or vaginalsecretions, an exudate, an effusion, or tissue. 65. The method of anypreceding embodiment, wherein the target nucleic acid is from a virus, afungus, a helminth, protozoa, a parasite, a malarial parasite, aPlasmodium parasites, a Toxoplasma parasites, and a Schistosomaparasites. 66. The method of any preceding embodiment, wherein thetarget nucleic acid is from influenza A virus, influenza B virus, RSV,dengue virus, West Nile virus, Hepatitis Virus C, Hepatitis Virus A,Hepatitis Virus B, papillomavirus, HIV, chlamydia, gonorrhea, syphilis,trichomoniasis, borrelia, zika virus, or a sepsis causing organism. 67.The method of any preceding embodiment, wherein the programmablenuclease is a Type V programmable nuclease. 68. The method of anypreceding embodiment, wherein the Type V programmable nuclease is aCas12. 69. The method of any preceding embodiment, wherein the Cas12 isCas12a, Cas12b, Cas12c, Cas12d, or Cas12e. 70. The method of anypreceding embodiment, wherein the programmable nuclease is a Type VIprogrammable nuclease. 71. The method of any preceding embodiment,wherein the Type VI programmable nuclease is a Cas13. 72. The method ofany preceding embodiment, wherein the Cas13 is Cas13a, Cas13b, Cas13c,Cas13d, or Cas13e. 73. The method of any preceding embodiment, whereinthe method comprises a second programmable nuclease. 74. The method ofany preceding embodiment, wherein the second programmable nuclease is aType V programmable nuclease. 75. The method of any precedingembodiment, wherein the Type V programmable nuclease is a Cas12. 76. Themethod of any preceding embodiment, wherein the Cas12 is Cas12a, Cas12b,Cas12c, Cas12d, or Cas12e. 77. The method of any preceding embodiment,wherein the second programmable nuclease is a Type VI programmablenuclease. 78. The method of any preceding embodiment, wherein the TypeVI programmable nuclease is a Cas13. 79. The method of any precedingembodiment, wherein the Cas13 is Cas13a, Cas13b, Cas13c, Cas13d, orCas13e. 80. The method of any preceding embodiment, wherein theprogrammable nuclease is a Cas14. 81. The method of any precedingembodiment, wherein the Cas14 is Cas14a, Cas14b, Cas14c, Cas14d, Cas14e,Cas14f, Cas14g, or Cas14h. 82. The method of any preceding embodiment,wherein the method is carried out in a device. 83. The method of anypreceding embodiment, wherein the device comprises: a sample chamber; adetection chamber fluidically connected to the sample chamber via apneumatic valve and comprising the programmable nuclease. 84. The methodof any preceding embodiment, wherein the device comprises anamplification chamber between the sample chamber and the detectionchamber. 85. The method of any preceding embodiment, wherein theamplification chamber is fluidically connected to the sample chamber andthe detection chamber via pneumatic valves. 86. The method of anypreceding embodiment, wherein the pneumatic valve is a PDMS pneumaticvalve. 87. The method of any preceding embodiment, wherein the pneumaticvalve comprises a channel perpendicular to a microfluidic channelproviding the fluidic connection between the sample chamber and thedetection chamber or the sample chamber and the sample chamber and theamplification chamber and the amplification chamber and the detectionchamber. 88. The method of any preceding embodiment, wherein the channelperpendicular to the microfluidic channel deflects downward uponapplication of air pressure through the channel perpendicular to themicrofluidic channel. 89. The method of any preceding embodiment,wherein lysing the sample occurs in the sample chamber for from 30seconds to 5 minutes. 90. The method of any preceding embodiment,wherein the method further comprises opening the pneumatic valve andmoving 1 to 10 ul from the sample chamber to the amplification chamber.91. The method of any preceding embodiment, wherein the method furthercomprises mixing the liquid in the amplification chamber. 92. The methodof any preceding embodiment, wherein the method further comprisesincubating for from 10 to 30 minutes. 93. The method of any precedingembodiment, wherein the method further comprises opening the pneumaticvalve and moving 1 to 10 ul from the amplification chamber to thedetection chamber. 94. The method of any preceding embodiment, whereinthe method further comprises mixing the liquid in the detection chamber.95. The method of any preceding embodiment, wherein the method furthercomprises incubating for from 1 minute to 10 minutes. 96. The method ofany preceding embodiment, wherein the assaying comprises measuring thesignal with a fluorescence reader or an electrochemical reader. 97. Themethod of any preceding embodiment, wherein the device is made of X. 98.The method of any preceding embodiment, wherein the device comprises asliding layer comprising a channel comprising: a channel; and a fixedlayer comprising: a sample chamber; a detection chamber, wherein thedetection chamber comprises a programmable nuclease. 99. The method ofany preceding embodiment, wherein the fixed layer further comprises anamplification chamber. 100. The method of any preceding embodiment,wherein the sliding layer is the lower layer. 101. The method of anypreceding embodiment, wherein the sliding layer is the upper layer. 102.The method of any preceding embodiment, wherein the channel, the samplechamber, the amplification chamber, the detection chamber, or anycombination thereof has an opening. 103. The method of any precedingembodiment, wherein the device further comprises a first side channelwith an opening aligned with the opening in the sample chamber, a secondside channel with an opening aligned with the opening in theamplification chamber, a third side channel with an opening aligned withthe opening in the detection chamber, or any combination thereof. 104.The method of any preceding embodiment, wherein the first side channel,the second side channel, and the third side channel are fluidicallyconnected to a mixing chamber. 105. The method of any precedingembodiment, wherein the mixing chamber comprises a pneumatic pump formixing, aspirating, and dispensing fluid in the device. 106. The methodof any preceding embodiment, wherein the sliding layer comprises asecond channel. 107. The method of any preceding embodiment, wherein thesecond channel comprises an opening. 108. The method of any precedingembodiment, wherein the fixed layer comprises from 1 to 10 additionalamplification chambers. 109. The method of any preceding embodiment,wherein the fixed layer comprises from 1 to 10 additional detectionchambers. 110. The method of any preceding embodiment, wherein the upperlayer is made of plastic polymers comprising poly-methacrylate (PMMA),cyclic olefin polymer (COP), cyclic olefin copolymer (COC), polyethylene(PE), high-density polyethylene (HDPE), polypropylene (PP); glass; orsilicon. 111. The method of any preceding embodiment, wherein the lowerlayer is made of plastic polymers comprising poly-methacrylate (PMMA),cyclic olefin polymer (COP), cyclic olefin copolymer (COC), polyethylene(PE), high-density polyethylene (HDPE), polypropylene (PP); glass; orsilicon. 112. The method of any preceding embodiment, wherein the methodcomprises one or more of the following steps: sliding the sliding layerto overlap the opening of the sample chamber with the opening of thechannel; moving the sample from the sample chamber into the channel;aspirating the sample from the channel into the first side channel andmixing; sliding the sliding layer to overlap the opening of the channelwith the opening of the amplification chamber; dispensing the sampleinto the amplification chamber; sliding the sliding layer to overlap theopening of the amplification chamber with the opening of the channel;moving the sample from the amplification chamber into the channel;aspirating the sample from the channel into the second side channel andnixing; sliding the sliding layer to overlap the opening of the channelwith the opening of the detection chamber; and dispensing the sampleinto the detection chamber. 113. The method of any preceding embodiment,wherein the device comprises from 1 to 10 additional detection chambers.114. The method of any preceding embodiment, wherein the devicecomprises from 1 to 10 additional amplification chambers. 115. Themethod of any preceding embodiment, wherein the detection chambercomprises a metal lead adapted for measurement of a change in current.116. The method of any preceding embodiment, wherein the device isadjacent to a thermal heater. 117. The method of any precedingembodiment, wherein the device comprises a region with a soft polymerattached to a metal element conducting heat. 118. The method of anypreceding embodiment, wherein the sample chamber holds a volume of from100 to 1000 μL. 119. The method of any preceding embodiment, wherein thedetection chamber holds a volume of from 1 to 100 μL. 120. The method ofany preceding embodiment, wherein the amplification chamber holds avolume of from 1 to 100 μL. 121. The method of any preceding embodiment,wherein the device further comprises a pH balancing chamber. 122. Themethod of any preceding embodiment, wherein the sample chamber has anopening for insertion of a sample. 123. The method of any precedingembodiment, wherein the sample chamber, the detection chamber, the andthe amplification chamber all have the same buffer. 124. The method ofany preceding embodiment, wherein the device comprises a chambercomprises the programmable nuclease; and the reporter comprising anucleic acid and a first molecule; and a lateral flow strip comprising:a first region comprising a second molecule; and a second regioncomprising an antibody, wherein the first region is upstream of thesecond region and the chamber is upstream of the lateral flow strip andwherein the first molecule binds to the second molecule. 125. The methodof any preceding embodiment, wherein the reporter further comprises afluorophore. 126. The method of any preceding embodiment, wherein thefirst molecule is conjugated directly to the fluorophore. 127. Themethod of any preceding embodiment, wherein the antibody on the secondregion is specific for the antibody coated on the detectable moiety.128. The method of any preceding embodiment, wherein the reporter issuspended in a buffer. 129. The method of any preceding embodiment,wherein the buffer comprises an aqueous solution, monovalent salts,divalent salts, or any combination thereof and wherein the buffercomprises a pH of from 6 to 8. 130. The method of any precedingembodiment, wherein the chamber comprises a second reporter comprising asecond nucleic acid, the first molecule, and a second fluorophore. 131.The method of any preceding embodiment, wherein the first molecule isconjugated directly to the second fluorophore. 132. The method of anypreceding embodiment, wherein the lateral flow strip comprises a thirdregion comprising a second antibody. 133. The method of any precedingembodiment, wherein the antibody binds the fluorophore and the secondantibody binds the second fluorophore. 134. The method of any precedingembodiment, wherein the lateral flow strip further comprises a samplepad upstream of the first region and downstream of the chamber. 135. Themethod of any preceding embodiment, wherein the sample pad comprises adetectable moiety. 136. The method of any preceding embodiment, whereinthe detectable moiety is a metal nanoparticle. 137. The method of anypreceding embodiment, wherein the metal nanoparticle is a goldnanoparticle. 138. The method of any preceding embodiment, wherein thedetectable moiety is coated in an antibody and wherein the antibodybinds to the fluorophore or wherein the antibody binds to the firstmolecule. 139. The method of any preceding embodiment, wherein thereporter, the second reporter, or both are immobilized to a surface ofthe chamber. 140. The method of any preceding embodiment, wherein thefirst molecule comprises a biotin. 141. The method of any precedingembodiment, wherein the second molecule comprises a streptavidin. 142.The method of any preceding embodiment, wherein the reporter, the secondreporter, or both further comprises a magnetic bead. 143. The method ofany preceding embodiment, wherein the chamber interfaces with a magnet.144. The method of any preceding embodiment, wherein the device isconnected to a sample prep device. 145. The method of any precedingembodiment, wherein from 1 to 10 devices are connected to a sample prepdevice. 146. The method of any preceding embodiment, wherein the sampleprep device comprises a sample chamber, an amplification chamber, or anycombination thereof, upstream of the reaction chamber. 147. The methodof any preceding embodiment, wherein the sample prep device comprises asample chamber, upstream, of an amplification chamber, upstream of thereaction chamber. 148. The method of any preceding embodiment, whereinthe sample chamber, the amplification chamber, the reaction chamber, andthe lateral flow strip are separated from each other by a substrate.149. The method of any preceding embodiment, wherein each chamber of thesample prep device comprises a notch preventing fluid flow. 150. Themethod of any preceding embodiment, wherein the sample prep devicecomprises a rotatable element and wherein the rotatable element controlsfluid flow through each chamber. 151. The method of any precedingembodiment, wherein the sample chamber comprises a lysis buffer. 152.The method of any preceding embodiment, wherein the amplifying comprisesisothermal amplification. 153. The method of any preceding embodiment,wherein the amplifying comprises recombinase polymerase amplification(RPA), transcription mediated amplification (TMA), strand displacementamplification (SDA), helicase dependent amplification (HDA), loopmediated amplification (LAMP), rolling circle amplification (RCA),single primer isothermal amplification (SPIA), ligase chain reaction(LCR), simple method amplifying RNA targets (SMART), improved multipledisplacement amplification (IMDA), or nucleic acid sequence-basedamplification (NASBA). 154. The method of any preceding embodiment,wherein the forward primer, the reverse primer, or both arephosphorothioated. 155. The method of any preceding embodiment 23,wherein the method has a limit of detection of at least 0.1 aM. 156. Themethod of any preceding embodiment, wherein the method has a limit ofdetection of at least 0.1 nM. 157. The method of any precedingembodiment, wherein the method has a limit of detection of at least 1nM. 158. The method of c1 any preceding embodiment, wherein the methodhas a positive predictive value of at least 75%, at least 80%, at least85%, at least 90%, at least 92%, at least 95%, at least 97%, at least99%, or 100%. 159. The method of any preceding embodiment, wherein themethod has a negative predictive value of at least 75%, at least 80%, atleast 85%, at least 90%, at least 92%, at least 95%, at least 97%, atleast 99%, or 100%. 160. The method of any preceding embodiment, whereinthe method further comprises adding an exonuclease to the sample. 161.The method of any preceding embodiment, wherein the device comprisesmore than one detection chambers each fluidically connected to oneamplification chamber. 162. The method of any preceding embodiment,wherein the device comprises more than one detection chambers eachfluidically connected to one sample chamber. 163. A device comprising: asample chamber; a detection chamber fluidically connected to the samplechamber via a pneumatic valve and comprising a programmable nuclease.164. The device of any preceding embodiment, wherein the devicecomprises an amplification chamber between the sample chamber and thedetection chamber. 165. The device of any preceding embodiment, whereinthe amplification chamber is fluidically connected to the sample chamberand the detection chamber via pneumatic valves. 166. A devicecomprising: a sample chamber; an amplification chamber fluidicallyconnected to the sample chamber via a first pneumatic valve; and adetection chamber fluidically connected to the amplification chamber viaa second pneumatic valve and comprising a programmable nuclease. 167.The device of any preceding embodiment, wherein the pneumatic valve is apolydimethylphenylsiloxane (PDMS) pneumatic valve, a urethane rubberpneumatic valve, or a silicon rubber pneumatic valve. 168. The device ofany preceding embodiment, wherein the pneumatic valve comprises achannel perpendicular to a microfluidic channel providing the fluidicconnection between the sample chamber and the detection chamber or thesample chamber and the sample chamber and the amplification chamber andthe amplification chamber and the detection chamber. 169. The device ofany preceding embodiment, wherein the channel perpendicular to themicrofluidic channel deflects downward upon application of positive ornegative air pressure and through the channel perpendicular to themicrofluidic channel. 170. A device comprising: a lower sliding layercomprising a channel comprising: a first channel; and a second channel;and an upper fixed layer comprising: a sample chamber; a detectionchamber, wherein the detection chamber comprises a programmablenuclease. 171. The device of any preceding embodiment, wherein the fixedlayer further comprises an amplification chamber. 172. A devicecomprising: a sliding layer comprising a channel comprising: a channel;and a fixed layer comprising: a sample chamber; an amplificationchamber; and a detection chamber, wherein the detection chambercomprises a programmable nuclease. 173. The device of any precedingembodiment, wherein the sliding layer is the lower layer. 174. Thedevice of any preceding embodiment, wherein the sliding layer is theupper layer. 175. The device of any preceding embodiment, wherein thefixed layer is the lower layer. 176. The device of any precedingembodiment, wherein the fixed layer is the upper layer. 177. The deviceof any preceding embodiment, wherein the channel, the sample chamber,the amplification chamber, the detection chamber, or any combinationthereof has an opening. 178. The device of any preceding embodiment,wherein the device further comprises a first side channel with anopening aligned with the opening in the sample chamber, a second sidechannel with an opening aligned with the opening in the amplificationchamber, a third side channel with an opening aligned with the openingin the detection chamber, or any combination thereof. 179. The device ofany preceding embodiment, wherein the first side channel, the secondside channel, and the third side channel are fluidically connected to amixing chamber. 180. The device of any preceding embodiment, wherein themixing chamber comprises a pneumatic pump for mixing, aspirating, anddispensing fluid in the device. 181. The device of any precedingembodiment, wherein the sliding layer comprises a second channel. 182.The device of any preceding embodiment, wherein the second channelcomprises an opening. 183. The device of any preceding embodiment,wherein the fixed layer comprises from 1 to 10 additional amplificationchambers. 184. The device of any preceding embodiment, wherein the fixedlayer comprises from 1 to 10 additional detection chambers. 185. Thedevice of any preceding embodiment, wherein the upper layer is made of aplastic polymer comprising poly-methacrylate (PMMA), cyclic olefinpolymer (COP), cyclic olefin copolymer (COC), polyethylene (PE),high-density polyethylene (HDPE), polypropylene (PP); a glass; or asilicon. 186. The device of any preceding embodiment, wherein the lowerlayer is made of a plastic polymer comprising poly-methacrylate (PMMA),cyclic olefin polymer (COP), cyclic olefin copolymer (COC), polyethylene(PE), high-density polyethylene (HDPE), polypropylene (PP); a glass; ora silicon. 187. The device of any preceding embodiment, wherein thedetection chamber comprises a reporter and a guide nucleic acid with aportion reverse complementary to a portion of a target nucleic acid.188. The device of any preceding embodiment, wherein the reportercomprises a nucleic acid, an affinity molecule, a detection molecule, aquencher, or any combination thereof. 189. The device of any precedingembodiment, wherein the nucleic acid is conjugated at one end to theaffinity molecule and the detection molecule. 190. The device of anypreceding embodiment, wherein the affinity molecule is biotin,glutathione, maltose, or chitin. 191. The device of any precedingembodiment, wherein the detection molecule is a fluorescent molecule. Anelectrochemical molecule, or an enzyme comprising horseradish peroxidaseaHRP) or alkaline phosphatase (AP). 192. The device of any precedingembodiment, wherein the fluorescent molecule is 6-fluorescein, IRDye700, TYE 665, ALEXA FLUOR 594, ATTO TM 633, or Iowa Black RQ. 193. Thedevice of any preceding embodiment, wherein the electrochemical moleculecomprises biotin, ferrocene, or invertase. 194. The device of anypreceding embodiment, wherein the quencher is IABkFQ or IRQC1N. 195. Thedevice of any preceding embodiment, wherein the reporter is immobilizedto the surface of the detection chamber. 196. The device of anypreceding embodiment, wherein the reporter is suspended in solution inthe detection chamber. 197. The device of any preceding embodiment,wherein the amplification chamber comprises reagents comprising adeoxynucleotide triphosphate, a forward primer, a reverse primer, areverse transcriptase, a T7 promoter, a T7 polymerase, UVSX (UVSY), anuclesase, a ribonuclease, or any combination thereof. 198. The deviceany preceding embodiment, wherein the sample chamber comprises a lysisbuffer. 199. The device of any preceding embodiment, wherein thereagents are lyophilized or vitrified. 200. The device of any precedingembodiment, wherein the reagents are suspended in a buffer. 201. Thedevice of any preceding embodiment, wherein the programmable nuclease islyophilized or vitrified. 202. The device of any preceding embodiment,wherein the programmable nuclease is suspended in a buffer. 203. Thedevice of any preceding embodiment, wherein the reporter and the guidenucleic acid are lyophilized or vitrified. 204. The device of anypreceding embodiment, wherein the reporter and the guide nucleic acidare suspended in a buffer. 205. The device of any preceding embodiment,wherein the buffer is a lysis buffer or an amplification buffer. 206.The device of any preceding embodiment, wherein the device is connectedto a pipette pump for aspirating, dispensing, and mixing fluids in thedevice. 207. The device of any preceding embodiment, wherein the deviceis made of a plastic polymer comprising poly-methacrylate (PMMA), cyclicolefin polymer (COP), cyclic olefin copolymer (COC), polyethylene (PE),high-density polyethylene (HDPE), polypropylene (PP); a glass; or asilicon. 208. The device of any preceding embodiment, wherein the devicecomprises from 1 to 10 additional detection chambers. 209. The device ofany preceding embodiment, wherein the detection chamber or at least onedetection chamber of the additional detection chambers comprises aunique guide RNA with a portion reverse complementary to a portion of atarget nucleic acid. 210. The device of any preceding embodiment,wherein the device comprises from 1 to 10 additional amplificationchambers. 211. The device of any preceding embodiment, wherein thedetection chamber is optically connected to a fluorescence measurementdevice. 212. The device of any preceding embodiment, wherein thedetection chamber comprises a metal lead adapted for measurement of achange in current. 213. The device of any preceding embodiment, whereinthe metal lead is connected to an electrochemical measurement device.214. The device of any preceding embodiment, wherein the device isadjacent to a thermal heater. 215. The device of any precedingembodiment, wherein the device comprises a region with a soft polymerattached to a metal element conducting heat. 216. The device of anypreceding embodiment, wherein the sample chamber holds a volume of from100 to 1000 μL. 217. The device of any preceding embodiment, wherein thedetection chamber holds a volume of from 1 to 100 μL. 218. The device ofany preceding embodiment, wherein the amplification chamber holds avolume of from 1 to 100 μL. 219. The device of any preceding embodiment,wherein the device further comprises a pH balancing chamber. 220. Thedevice of any preceding embodiment, wherein the detection chambercomprises from 1 nM to 100 nM of target nucleic acids. 221. The deviceof any preceding embodiment, wherein the detection chamber comprisesfrom 1 nM to 1000 nM of total nucleic acids. 222. The device of anypreceding embodiment, wherein the detection chamber comprises from 10 to25 nM of target nucleic acids. 223. The device of any precedingembodiment, wherein the detection chamber comprises from 10 nM to 1000nM of reporter. 224. The device of any preceding embodiment, wherein thedetection chamber comprises from 100 to 500 nM of reporter. 225. Thedevice of any preceding embodiment, wherein the detection chambercomprises a plurality of guide RNAs. 226. The device of any precedingembodiment, wherein the plurality of guide RNAs have the same sequence.227. The device of any preceding embodiment, wherein the sequence of atleast one guide RNA of the plurality of guide RNAs is unique. 228. Thedevice of any preceding embodiment, wherein at least one guide RNAs ofthe plurality of guide RNAs has a portion reverse complementary to aportion of a target nucleic acid different than a second RNA of theplurality of guide RNAs. 229. The device of any preceding embodiment,wherein the plurality of guide RNAs comprise at least 20 guide RNAs.230. The device of any preceding embodiment, wherein each of the 20guide RNAs has a portion reverse complementary to a portion of adifferent target nucleic acid. 231. The device of any precedingembodiment, wherein the sample chamber has an opening for insertion of asample. 232. The device of any preceding embodiment, wherein the samplechamber, the detection chamber, the and the amplification chamber allhave the same buffer. 233. A device comprising: a chamber comprising aprogrammable nuclease; and a reporter comprising a nucleic acid and afirst molecule; and a lateral flow strip comprising: a first regioncomprising a second molecule; and a second region comprising anantibody, wherein the first region is upstream of the second region andthe chamber is upstream of the lateral flow strip and wherein the firstmolecule binds to the second molecule. 234. The device of any precedingembodiment, wherein the reporter further comprises a fluorophore. 235.The device of any preceding embodiment, wherein the first molecule isconjugated directly to the fluorophore. 236. The device of any precedingembodiment, wherein the antibody on the second region is specific forthe antibody coated on the detectable moiety. 237. The device of anypreceding embodiment, wherein the reporter is suspended in a buffer.238. The device of any preceding embodiment, wherein the buffer iscomprises an aqueous solution, monovalent salts, divalent salts, or anycombination thereof and wherein the buffer comprises a pH of from 6 to8. 239. The device of any preceding embodiment, wherein the chambercomprises a second reporter comprising a second nucleic acid, the firstmolecule, and a second fluorophore. 240. The device of any precedingembodiment, wherein the first molecule is conjugated directly to thesecond fluorophore. 241. The device of any preceding embodiment, whereinthe lateral flow strip comprises a third region comprising a secondantibody. 242. The device of any preceding embodiment, wherein theantibody binds the fluorophore and the second antibody binds the secondfluorophore. 243. The device of any preceding embodiment, wherein thelateral flow strip further comprises a sample pad upstream of the firstregion and downstream of the detection chamber. 244. The device of anypreceding embodiment, wherein the sample pad comprises a detectablemoiety. 245. The device of any preceding embodiment, wherein thedetectable moiety is a nanoparticle. 246. The device of any precedingembodiment, wherein the nanoparticle is a metal nanoparticle, a goldnanoparticle, a silica particle, a silica-coated paramegnetic particle,a fluorescent particle, or any combination thereof. 247. The device ofany preceding embodiment, wherein the detectable moiety is coated in anantibody and wherein the antibody binds to the fluorophore or whereinthe antibody binds to the first molecule. 248. The device of anypreceding embodiment, wherein the reporter, the second reporter, or bothare immobilized to a surface of the chamber. 249. The device of anypreceding embodiment, wherein the first molecule comprises a biotin,glutathione, maltose, chitin, or any combination thereof 250. The deviceof any preceding embodiment, wherein the second molecule comprises astreptavidin, glutathione-S-transferase, maltose-binding protein,chitin-binding protein, or any combination thereof. 251. The device ofany preceding embodiment, wherein the reporter comprises 6-fluoresceinor digoxigenin. 252. The device of any preceding embodiment, wherein thesecond reporter comprises 6-fluorescein or digoxigenin. 253. The deviceof any preceding embodiment, wherein the reporter, the second reporter,or both further comprises a quencher. 254. The device of any precedingembodiment, wherein the quencher is IABkFQ or IRQC1N. 255. The device ofany preceding embodiment, wherein the reporter, the second reporter, orboth further comprises a magnetic bead. 256. The device of any precedingembodiment, wherein the chamber interfaces with a magnet. 257. Thedevice of any preceding embodiment, wherein the device is connected to asample prep device. 258. The device of any preceding embodiment, whereinfrom 1 to 10 devices are connected to a sample prep device. 259. Thedevice of any preceding embodiment, wherein the sample prep devicecomprises a sample chamber, an amplification chamber, or any combinationthereof, upstream of the reaction chamber. 260. The device of anypreceding embodiment, wherein the sample prep device comprises a samplechamber, upstream, of an amplification chamber, upstream of the reactionchamber. 261. The device of any preceding embodiment, wherein the samplechamber, the amplification chamber, the reaction chamber, and thelateral flow strip are separated from each other by a substrate. 262.The device of any preceding embodiment, wherein each chamber of thesample prep device comprises a notch preventing fluid flow. 263. Thedevice of any preceding embodiment, wherein the sample prep devicecomprises a rotatable element and wherein the rotatable element controlsfluid flow through each chamber. 264. The device of any precedingembodiment, wherein the sample chamber comprises a lysis buffer. 265.The device of any preceding embodiment, wherein the sample chambercomprises a biological sample. 266. The device of any precedingembodiment, wherein the biological sample comprises a target nucleicacid. 267. The device of any preceding embodiment, wherein thebiological sample is blood, serum, plasma, saliva, urine, mucosalsample, peritoneal sample, cerebrospinal fluid, gastric secretions,nasal secretions, sputum, pharyngeal exudates, urethral or vaginalsecretions, an exudate, an effusion, or tissue. 268. The device of anypreceding embodiment, wherein the target nucleic acid is from a virus, afungus, a helminth, protozoa, a parasite, a malarial parasite, aPlasmodium parasites, a Toxoplasma parasites, and a Schistosomaparasites. 269. The device of any preceding embodiment, wherein thetarget nucleic acid is from influenza A virus, influenza B virus, RSV,dengue virus, West Nile virus, Hepatitis Virus C, Hepatitis Virus A,Hepatitis Virus B, papillomavirus, HIV, chlamydia, gonorrhea, syphilis,trichomoniasis, borrelia, zika virus, or a sepsis causing organism. 270.The device of any preceding embodiment, wherein the programmablenuclease is a Type V programmable nuclease. 271. The device of anypreceding embodiment, wherein the Type V programmable nuclease is aCas12. 272. The device of any preceding embodiment, wherein the Cas12 isCas12a, Cas12b, Cas12c, Cas12d, or Cas12e. 273. The device of anypreceding embodiment, wherein the programmable nuclease is a Type VIprogrammable nuclease. 274. The device of any preceding embodiment,wherein the Type VI programmable nuclease is a Cas13. 275. The device ofany preceding embodiment, wherein the Cas13 is Cas13a, Cas13b, Cas13c,Cas13d, or Cas13e. 276. The device of any preceding embodiment, whereinthe detection chamber comprises a second programmable nuclease. 277. Thedevice of any preceding embodiment, wherein the chamber comprises asecond programmable nuclease. 278. The device of any precedingembodiment, wherein the second programmable nuclease is a Type Vprogrammable nuclease. 279. The device of any preceding embodiment,wherein the Type V programmable nuclease is a Cas12. 280. The device ofany preceding embodiment, wherein the Cas12 is Cas12a, Cas12b, Cas12c,Cas12d, or Cas12e. 281. The device of any preceding embodiment, whereinthe second programmable nuclease is a Type VI programmable nuclease.282. The device of any preceding embodiment, wherein the Type VIprogrammable nuclease is a Cas13. 283. The device of any precedingembodiment wherein the Cas13 is Cas13a, Cas13b, Cas13c, Cas13d, orCas13e. 284. The device of any preceding embodiment, wherein theprogrammable nuclease is a Cas14. 285. The device of any precedingembodiment, wherein the Cas14 is Cas14a, Cas14b, Cas14c, Cas14d, Cas14e,Cas14f, Cas14g, or Cas14h. 286. The device of any preceding embodiment,wherein the nucleic acid is a single stranded nucleic acid. 287. Thedevice of any preceding embodiment, wherein the single stranded nucleicacid is single stranded DNA. 288. The device of any precedingembodiment, wherein the single stranded nucleic acid is single strandedRNA. 289. The device of any preceding embodiment, wherein the devicecomprises more than one detection chambers each fluidically connected toone amplification chamber. 290. The device of any preceding embodiment,wherein the device comprises more than one detection chambers eachfluidically connected to one sample chamber. 291. The device of anypreceding embodiment, wherein the detection chamber comprises aplurality of guide nucleic acids, wherein the plurality of guide nucleicacids target at least 20 different target nucleic acids. 292. The deviceof any preceding embodiment, wherein the device comprises at least 20detection chambers.

The following embodiments recite permutations of combinations offeatures disclosed herein. In some cases, permutations of combinationsof features disclosed herein are non-limiting. In other casespermutations of combinations of features disclosed herein are limiting.Other permutations of combinations of features are also contemplated. Inparticular, each of these numbered embodiments is contemplated asdepending from or relating to every previous or subsequent numberedembodiment, independent of their order as listed. 1. A device formeasuring a signal comprising: i) a first chamber comprising a sampleand a buffer for lysing the sample; ii) a second chamber, fluidicallyconnected by a first pneumatic valve to the first chamber, wherein thesecond chamber comprises a programmable nuclease and a reportercomprising a nucleic acid and a detection moiety, and wherein the secondchamber is coupled to a measurement device for measuring the signal fromthe detection moiety produced by cleavage of the nucleic acid of thereporter. 2. The device of claim 1, wherein the device furthercomprises: iii) a third chamber fluidically connected by the firstpneumatic valve to the first chamber and connected by a second pneumaticvalve to the second chamber. 3. The device of claim 1, wherein the firstpneumatic valve fluidically connecting the first chamber and the secondchamber comprises a first channel adjacent to a first microfluidicchannel connecting the first chamber and the second chamber. 4. Thedevice of claim 2, wherein the first pneumatic valve fluidicallyconnecting the first chamber and the third chamber comprises a secondchannel adjacent to a second microfluidic channel connecting the firstchamber and the third chamber. 5. The device of claim 2, wherein thesecond pneumatic valve fluidically connecting the second chamber and thethird chamber comprises a third channel adjacent to a third microfluidicchannel connecting the second chamber and the third chamber. 6. Thedevice of any one of claims 2-5, wherein the first channel, the secondchannel, or the third channels are connected to an air manifold. 7. Thedevice of any one of claims 1-6, wherein more than one chambercomprising a programmable nuclease and a reporter are fluidicallyconnected to a single chamber comprising the sample. 8. The device ofany one of claims 1-7, wherein more than one chamber comprising aprogrammable nuclease and a reporter are fluidically connected to asingle chamber comprising a forward primer, a reverse primer, a dNTP,and a polymerase. 9. A device for measuring a signal comprising: asliding layer comprising a channel with an opening at a first end of thechannel and an opening at a second end of the channel; and a fixed layercomprising: i) a first chamber having an opening; ii) a second chamberhaving an opening, wherein the second chamber comprises a programmablenuclease and a reporter comprising a nucleic acid and a detectionmoiety; iii) a first side channel having an opening aligned with theopening of the first chamber; and iv) a second side channel having anopening aligned with the opening of the second chamber, wherein thesliding layer and the fixed layer move relative to each other tofluidically connect the first chamber and the first side channel via theopening at the first end of the channel, the opening at the second endof the channel, the opening of the first chamber, and the opening of thefirst side channel, and wherein the sliding layer and the fixed layermove relative to each other to fluidically connect the second chamberand the second side channel via the opening at the first end of thechannel, the opening at the second end of the channel, the opening ofthe second chamber, and the opening of the second side channel. 10. Thedevice of claim 9, wherein the fixed layer further comprises i) a thirdchamber having an opening; and. ii) a third side channel having anopening aligned with the opening of the third chamber, wherein thesliding layer and the fixed layer move relative to each other tofluidically connect the third chamber and the third side channel via theopening at the first end of the channel, the opening at the second endof the channel, the opening of the third chamber, and the opening of thethird side channel. 11. The device of any one of claims 9-10, whereinthe second chamber is coupled to a measurement device for measuring thesignal from the detection moiety produced by cleavage of the nucleicacid of the reporter. 12. The device of any one of claims 9-11, whereinthe opening of the first end of the channel overlaps with the opening ofthe first chamber and the opening of the second end of the channeloverlaps with the opening of the first side channel. 13. The device ofany one of claims 9-12, wherein the opening of the first end of thechannel overlaps with the opening of the second chamber and the openingof the second end of the channel overlaps with the opening of the secondside channel. 14. The device of any one of claims 10-13, wherein theopening of the first end of the channel overlaps with the opening of thethird chamber and the opening of the second end of the channel overlapswith the opening of the third channel. 15. The device of any one ofclaims 9-14, wherein the first side channel, the second side channel,and the third side channel are fluidically connected to a mixingchamber. 16. The device of any one of claims 2-8 or 10-15, wherein thethird chamber comprises a forward primer, a reverse primer, a dNTP, anNTP, a polymerase, a reverse transcriptase, a T7 polymerase, or anycombination thereof. 17. The device of claim 16, wherein the forwardprimer, the reverse primer, or both comprises a T7 promoter. 18. Thedevice of any one of claims 1-17, wherein the second chamber comprises aguide nucleic acid. 19. The device of any one of claims 1-18, whereinthe programmable nuclease, the reporter, the guide nucleic acid, theforward primer, the reverse primer, the dNTP, the NTP, the polymerase,the reverse transcriptase, the T7 promoter, the T7 polymerase, or anycombination thereof is lyophilized or vitrified. 20. The device of anyone of claims 1-19, wherein the second chamber is optically connected toa spectrophotometric measurement device or a fluorescence measurementdevice. 21. The device of any one of claims 1-19, wherein the secondchamber comprises a metal lead adapted for measurement of a change incurrent. 22. The device of any one of claims 1-21, wherein the firstchamber holds a volume of about 200 μL, the second chamber holds avolume of about 20 μL, and the third chamber holds a volume of about 20μL. 23. The device of any one of claims 1-22, wherein the second chambercomprises a plurality of guide RNAs. 24. The device of any one of claims1-23, wherein the device comprises from 2 to 20 chambers comprising aprogrammable nuclease, a guide nucleic acid, and a reporter, wherein adetection chamber of the from 2 to 20 chambers comprises a unique guidenucleic acid. 25. The device of any one of claims 1-24, wherein thereporter is a hybrid reporter having at least one ribonucleotide and atleast one deoxyribonucleotide. 26. The device of any one of claim 1-25,wherein the reporter is immobilized to a surface. 27. The device ofclaim 26, wherein the surface is a surface of the first chamber or asurface of a bead. 28. A device comprising: a chamber comprising i) aprogrammable nuclease; and ii) an immobilized reporter comprising anucleic acid, an affinity molecule, and a detection moiety; and alateral flow strip comprising: i) a first region comprising a capturemolecule specific for the affinity molecule; and ii) a second regioncomprising an antibody, wherein the first region is upstream of thesecond region and the chamber is upstream of the lateral flow strip andwherein the first molecule binds to the second molecule. 29. The deviceof claim 28, wherein the first molecule is conjugated to a 3′ end or a5′ end of the nucleic acid, and wherein the first molecule is directlyconjugated to the detection moiety. 30. The device of any one of claims28-29, wherein the detection moiety comprises a fluorophore. 31. Thedevice of any one of claims 28-30, wherein the antibody on the secondregion is specific for an antibody-coated nanoparticle. 32. The deviceof claim 31, wherein the antibody-coated nanoparticle binds thefluorophore. 33. The device of any one of claims 28-32, wherein thechamber further comprises a second immobilized reporter comprising asecond nucleic acid, a second detection moiety, and the first molecule.34. The device of claim 33, wherein the first molecule is conjugated toa 3′ end or a 5′ end of the second nucleic acid, and wherein the firstmolecule is directly conjugated to the second detection moiety. 35. Thedevice of any one of claims 28-34, wherein the lateral flow stripcomprises a third region comprising a second antibody. 36. The device ofclaim 35, wherein the antibody binds the fluorophore and the secondantibody binds the second fluorophore. 37. The device of any one ofclaims 28-36, wherein the immobilized reporter, the second immobilizedreporter, or both are conjugated to a magnetic bead. 38. The device ofany one of claims 28-37, wherein the chamber interfaces with a magnet.39. The device of any one of claims 28-38, wherein the device isconnected to a sample prep device comprising a sample chamber, upstream,of an amplification chamber, upstream of the chamber. 40. The device ofclaim 39, wherein the sample chamber, the amplification chamber, thereaction chamber, and the lateral flow strip are separated by asubstrate. 41. The device of any one of claims 39-40, wherein eachchamber of the sample prep device comprises a notch preventing fluidflow. 42. The device of any one of claims 39-41, wherein the sample prepdevice comprises a rotatable element and wherein the rotatable elementcontrols fluid flow between chambers. 43. A method of detecting apresence or an absence of a target nucleic acid in a sample, the methodcomprising: contacting a first volume to a second volume, wherein thefirst volume comprises the sample and the second volume comprises: i) aguide nucleic acid having at least 10 nucleotides reverse complementaryto a target nucleic acid in the sample; and ii) a programmable nucleaseactivated upon binding of the guide nucleic acid to the target nucleicacid; iii) a reporter comprising a nucleic acid and a detection moiety,wherein the second volume is at least 4-fold greater than the firstvolume; and detecting the presence or the absence of the target nucleicacid by measuring a signal produced by cleavage of the nucleic acid ofthe reporter, wherein cleavage occurs when the programmable nuclease isactivated. 44. The device of any one of claims 1-42 for use in a methodof detecting a presence of an absence of a target nucleic acid in asample, the method comprising: contacting a first volume to a secondvolume, wherein the first volume comprises the sample and the secondvolume comprises: i) a guide nucleic acid having at least 10 nucleotidesreverse complementary to a target nucleic acid in the sample; and ii) aprogrammable nuclease activated upon binding of the guide nucleic acidto the target nucleic acid; iii) a reporter comprising a nucleic acidand a detection moiety, wherein the second volume is at least 4-foldgreater than the first volume; and detecting the presence or the absenceof the target nucleic acid by measuring a signal produced by cleavage ofthe nucleic acid of the reporter, wherein cleavage occurs when theprogrammable nuclease is activated. 45. A method comprising of detectinga presence of an absence of a first target nucleic acid, a second targetnucleic acid, or both in a sample, the method comprising: contacting thesample to i) a first guide nucleic acid having at least 10 nucleotidesreverse complementary to the first target nucleic acid from an organismand a first programmable nuclease activated upon binding of the firstguide nucleic acid to the first target nucleic acid; and ii) a secondguide nucleic acid having at least 10 nucleotides reverse complementaryto the second target nucleic acid from a drug resistant allele of theorganism and a second programmable nuclease activated upon binding ofthe second guide nucleic acid to the second target nucleic acid, whereinthe first programmable nuclease and the second programmable nuclease aredifferent; detecting a presence or an absence of the first targetnucleic acid by measuring a first signal produced by cleavage of anucleic acid of a first reporter, wherein cleavage occurs when the firstprogrammable nuclease is activated; and detecting a presence or anabsence of the second target nucleic acid by measuring a second signalproduced by cleavage of a nucleic acid of the second reporter, whereincleavage occurs when the second programmable nuclease is activated. 46.The device of any one of claims 1-42 for use in a method of detecting apresence of an absence of a first target nucleic acid, a second targetnucleic acid, or both in a sample, the method comprising: contacting thesample to i) a first guide nucleic acid having at least 10 nucleotidesreverse complementary to the first target nucleic acid from an organismand a first programmable nuclease activated upon binding of the firstguide nucleic acid to the first target nucleic acid; and ii) a secondguide nucleic acid having at least 10 nucleotides reverse complementaryto the second target nucleic acid from a drug resistant allele of theorganism and a second programmable nuclease activated upon binding ofthe second guide nucleic acid to the second target nucleic acid, whereinthe first programmable nuclease and the second programmable nuclease aredifferent; detecting a presence or an absence of the first targetnucleic acid by measuring a first signal produced by cleavage of anucleic acid of a first reporter, wherein cleavage occurs when the firstprogrammable nuclease is activated; and detecting a presence or anabsence of the second target nucleic acid by measuring a second signalproduced by cleavage of a nucleic acid of the second reporter, whereincleavage occurs when the second programmable nuclease is activated 47.The method of any one of claims 45-46, wherein the first target nucleicacid and the second target nucleic acid are different. 48. The method ofany one of claims 45-47, wherein the nucleic acid of the first reporteris a DNA nucleic acid and wherein the nucleic acid of the secondreporter is an RNA nucleic acid. 49. A method of detecting a targetnucleic acid in a sample, the method comprising: contacting the sampleto: i) a guide nucleic acid having at least 10 nucleotides reversecomplementary to the target nucleic acid; and ii) a programmablenuclease activated upon binding of the guide nucleic acid to the targetnucleic acid; iii) a hybrid reporter comprising a detection moiety and anucleic acid having at least one ribonucleotide and at least onedeoxyribonucleotide; detecting a presence or an absence of the targetnucleic acid by measuring a signal produced by cleavage of the nucleicacid of the hybrid reporter, wherein cleavage occurs when theprogrammable nuclease is activated. 50. Any device provided herein foruse in a method of detecting a target nucleic acid in a sample, themethod comprising: contacting the sample to: i) a guide nucleic acidhaving at least 10 nucleotides reverse complementary to the targetnucleic acid; and ii) a programmable nuclease activated upon binding ofthe guide nucleic acid to the target nucleic acid; iii) a hybridreporter comprising a detection moiety and a nucleic acid having atleast one ribonucleotide and at least one deoxyribonucleotide; detectinga presence or an absence of the target nucleic acid by measuring asignal produced by cleavage of the nucleic acid of the hybrid reporter,wherein cleavage occurs when the programmable nuclease is activated. 51.A method for identifying a treatment for a subject comprising: measuringa signal by: contacting a sample comprising a target nucleic acid fromthe subject to: i) a guide nucleic acid having at least 10 nucleotidesreverse complementary to the target nucleic acid; and ii) a programmablenuclease activated upon binding of the guide nucleic acid to the targetnucleic acid; iii) a reporter comprising a nucleic acid and a detectionmoiety; and measuring the signal produced by cleavage of the nucleicacid of the reporter, wherein cleavage occurs when the programmablenuclease is activated; and identifying the treatment to administer tothe subject. 52. The device of any one of claims 1-42 for use in amethod for identifying a treatment for a subject comprising: measuring asignal by: contacting a sample comprising a target nucleic acid from thesubject to: i) a guide nucleic acid having at least 10 nucleotidesreverse complementary to the target nucleic acid; and ii) a programmablenuclease activated upon binding of the guide nucleic acid to the targetnucleic acid; iii) a reporter comprising a nucleic acid and a detectionmoiety; and measuring the signal produced by cleavage of the nucleicacid of the reporter, wherein cleavage occurs when the programmablenuclease is activated; and identifying the treatment to administer tothe subject 53. The method of any one of claims 45-52, wherein thesample is in a first volume and wherein the guide nucleic acid, theprogrammable nuclease, and the reporter are in a second volume. 54. Themethod of claim 53, wherein the second volume is at least 4-fold greaterthan the first volume. 55. The method of any one of claims 43-44 or53-54, wherein the second volume is at least 10-fold greater than thefirst volume. 56. The method of any one of claims 43-48 or 51-55,wherein the reporter is a hybrid reporter having at least oneribonucleotide and at least one deoxyribonucleotide. 57. The method ofany one of claims 43-56, wherein the method comprises amplifying thetarget nucleic acid, reverse transcribing the target nucleic acid, invitro transcription of the target nucleic acid, or any combinationthereof. 58. The method of claim 57, wherein the amplifying comprisesusing a phosphorothioated forward primer, a phosphorothioated reverseprimer, or both. 59. The method of any one of claims 57-58, wherein theamplifying comprises isothermal amplification. 60. The method of any oneof claims 57-58, wherein the amplifying comprises thermal amplification.61. The method of any one of claims 57-58, wherein the amplifyingcomprises recombinase polymerase amplification (RPA), transcriptionmediated amplification (TMA), strand displacement amplification (SDA),helicase dependent amplification (HDA), loop mediated amplification(LAMP), rolling circle amplification (RCA), single primer isothermalamplification (SPIA), ligase chain reaction (LCR), simple methodamplifying RNA targets (SMART), or improved multiple displacementamplification (IMDA), or nucleic acid sequence-based amplification(NASBA). 62. The method of claim 61, wherein the amplifying comprisesrecombinase polymerase amplification (RPA). 63. The method of claim 61,wherein the amplifying comprises loop mediated amplification (LAMP). 64.The method of any one of claims 57-63, wherein the amplifying the targetnucleic acid, the reverse transcribing the target nucleic acid, the invitro transcription of the target nucleic acid, or any combinationthereof is in the same reaction as the detecting and the measuring. 65.The method of any one of claims 43-64, wherein the method furthercomprises removing non-target nucleic acids with an exonuclease. 66. Themethod of any one of claims 43-65, wherein the nucleic acid of thereporter is conjugated at its 3′ end or 5′ end to an affinity molecule,wherein the affinity molecule is directly conjugated to the detectionmoiety. 67. The method of any one of claims 43-66, wherein the guidenucleic acid, the programmable nuclease, and the reporter are present ina single chamber. 68. The method of claim 67, wherein the single chamberis fluidically connected to a second chamber via a first pneumaticvalve, wherein the second chamber comprises the sample. 69. The methodof claim 68, wherein a third chamber is positioned between the secondchamber and the single chamber, wherein the third chamber comprises adNTP, a forward primer, a reverse primer, and a polymerase. 70. Themethod of claim 69, wherein the third chamber is fluidically connectedto the single chamber via a second pneumatic valve and wherein the thirdchamber is fluidically connected to the second chamber via a thirdpneumatic valve. 71. The method of any one of claims 69-70, wherein themethod further comprises: opening the third pneumatic valve and moving 1to 10 μL of the sample from the second chamber to the third chamber; andopening the second pneumatic valve and moving 1 to 10 μL of the samplefrom the third chamber to the single chamber, or opening the firstpneumatic valve and moving 1 to 10 μL of the sample from the secondchamber to the single chamber. 72. The method of any one of claims67-71, wherein the method further comprises incubating the sample in thesingle chamber for from 1 minute to 10 minutes. 73. The method of claim67, wherein the single chamber has an opening. 74. The method of any oneof claim 67 or 73, wherein the single chamber and a second chamberhaving an opening are positioned in a fixed layer, wherein the secondchamber comprises the sample, and wherein the fixed layer is coupled toa sliding layer comprising a channel having a first opening and a secondopening. 75. The method of claim 74, wherein the fixed layer furthercomprises a third chamber having an opening, wherein the third chambercomprises a dNTP, a forward primer, a reverse primer, and a polymerase.76. The method of claim 75, wherein the opening in the second chamber isaligned with an opening in a first side channel, the opening in thethird chamber is aligned with an opening in a second side channel, andthe opening in the single chamber is aligned with an opening in a thirdside channel. 77. The method of any one of claims 73-76, wherein themethod comprises one or more of the following steps: sliding the slidinglayer to overlap the opening of the second chamber with the opening ofthe channel; moving the sample from the second chamber into the channel;aspirating the sample from the channel into the first side channel andmixing; sliding the sliding layer to overlap the opening of the channelwith the opening of the third chamber; dispensing the sample into thethird chamber; moving the sample from the third chamber into thechannel; aspirating the sample from the channel into the second sidechannel and mixing; sliding the sliding layer to overlap the opening ofthe channel with the opening of the single chamber; and dispensing thesample into the single chamber. 78. The method of any one of claims73-76, wherein the method comprises one or more of the following steps:sliding the sliding layer to overlap the opening of the second chamberwith the opening of the channel; moving the sample from the secondchamber into the channel; aspirating the sample from the channel intothe first side channel and mixing; sliding the sliding layer to overlapthe opening of the channel with the opening of the single chamber; anddispensing the sample into the single chamber. 79. The method of any oneof claims 43-78, wherein the measuring comprises fluorescence imaging,spectrophotometry, or electrochemical measurements. 80. The method ofany one of claims 43-79, wherein the programmable nuclease, thereporter, the guide nucleic acid, or any combination thereof arelyophilized or vitrified. 81. The method of any one of claims 43-80,wherein the guide nucleic acid comprises from 2 to 20 guide RNAs andwherein a guide RNA of the from 2 to 20 guide RNAs is a unique guideRNA. 82. The method of any one of claim 43-81, wherein the reporter isimmobilized to a surface in the single chamber. 83. The method of claim82, wherein the surface is a surface of the single chamber or a surfaceof a bead. 84. Any one of the devices described herein or any one of themethods described herein, wherein the target nucleic acid is frominfluenza A virus, influenza B virus, RSV, dengue virus, West Nilevirus, Hepatitis Virus C, Hepatitis Virus A, Hepatitis Virus B,papillomavirus, HIV, chlamydia, gonorrhea, syphilis, trichomoniasis,borrelia, zika virus, or a sepsis causing organism. 85. The device ormethod of any one of claims 1-84, wherein the programmable nuclease is aprogrammable Type V CRISPR/Cas enzyme. 86. The device or method of claim85, wherein the programmable Type V CRISPR/Cas enzyme is a programmableCas12 nuclease. 87. The device or method of claim 86, wherein theprogrammable Cas12 nuclease is Cas12a, Cas12b, Cas12c, Cas12d, orCas12e. 88. The device or method of claim 85, wherein programmable TypeV CRISPR/Cas enzyme is a programmable Cas14 nuclease. 89. The device ormethod of claim 88, wherein the programmable Cas14 nuclease is Cas14a,Cas14b, Cas14c, Cas14d, Cas14e, Cas14f, Cas14g, or Cas14h. 90. Thedevice or method of any one of claims 1-89, wherein the programmablenuclease is a programmable Type VI CRISPR/Cas enzyme. 91. The device ormethod of claim 90, wherein the programmable Type VI CRISPR/Cas enzymeis a programmable Cas13 nuclease. 92. The device or method of claim 91,wherein the programmable Cas13 nuclease is Cas13a, Cas13b, Cas13c,Cas13d, or Cas13e. 93. The use of a programmable nuclease in a devicefor measuring a signal, wherein the device comprises: i) a first chambercomprising a sample and a buffer for lysing the sample; ii) a secondchamber, fluidically connected by a first pneumatic valve to the firstchamber, wherein the second chamber comprises the programmable nucleaseand a reporter comprising a nucleic acid and a detection moiety, andwherein the second chamber is coupled to a measurement device formeasuring the signal from the detection moiety produced by cleavage ofthe nucleic acid of the reporter. 94. The use of a programmable nucleasein a device for measuring a signal, wherein the device comprises: asliding layer comprising a channel with an opening at a first end of thechannel and an opening at a second end of the channel; and a fixed layercomprising: iii) a first chamber having an opening; iv) a second chamberhaving an opening, wherein the second chamber comprises the programmablenuclease and a reporter comprising a nucleic acid and a detectionmoiety; v) a first side channel having an opening aligned with theopening of the first chamber; and vi) a second side channel having anopening aligned with the opening of the second chamber, wherein thesliding layer and the fixed layer move relative to each other tofluidically connect the first chamber and the first side channel via theopening at the first end of the channel, the opening at the second endof the channel, the opening of the first chamber, and the opening of thefirst side channel, and wherein the sliding layer and the fixed layermove relative to each other to fluidically connect the second chamberand the second side channel via the opening at the first end of thechannel, the opening at the second end of the channel, the opening ofthe second chamber, and the opening of the second side channel. 95. Theuse of a programmable nuclease in a device for measuring a signal,wherein the device comprises: a chamber comprising i) a programmablenuclease; and ii) an immobilized reporter comprising a nucleic acid, anaffinity molecule, and a detection moiety; and a lateral flow stripcomprising: i) a first region comprising a capture molecule specific forthe affinity molecule; and ii) a second region comprising an antibody,wherein the first region is upstream of the second region and thechamber is upstream of the lateral flow strip and wherein the firstmolecule binds to the second molecule. 96. The use of a hybrid reporterin a method of detecting a target nucleic acid in a sample, the methodcomprising: contacting the sample to: i) a guide nucleic acid having atleast 10 nucleotides reverse complementary to the target nucleic acid;and ii) a programmable nuclease activated upon binding of the guidenucleic acid to the target nucleic acid; iii) a hybrid reportercomprising a detection moiety and a nucleic acid having at least oneribonucleotide and at least one deoxyribonucleotide; detecting apresence or an absence of the target nucleic acid by measuring a signalproduced by cleavage of the nucleic acid of the hybrid reporter, whereincleavage occurs when the programmable nuclease is activated.

EXAMPLES

The following examples are illustrative and non-limiting to the scope ofthe devices, systems, fluidic devices, kits, and methods describedherein.

Example 1 Testing of One Communicable Disease

A biological sample from an individual is tested to determine whetherthe individual has a communicable disease. The biological sample istested to detect the presence or absence of a target nucleic acidindicative of a bacteria or a virus responsible for the communicabledisease.

A biological sample of urine of an individual is obtained and thebiological sample is applied to the reagents described herein in areagent chamber provided in a kit. The reagents are comprised of a guidenucleic acid targeting a nucleic acid present in and specific to thebacteria or the virus, a programmable nuclease, and a single strandeddetector nucleic acid with a detection moiety. The virus responsible forthe communicable disease, and the target nucleic acid from the bacteriaor the virus binds to the guide nucleic acid and activates theprogrammable nuclease to cleave the target nucleic acid and the singlestranded detector nucleic acid, is found in the biological sample. Insome examples, a CRISPR/Cas nuclease is used as the programmablenuclease.

After the sample and the reagents are contacted for a predeterminedtime, the reacted sample and reagents are applied to a sample pad regionon a support medium. The support medium is comprised of a lateral flowassay test strip encased in a protective housing with openings for thesample pad region to apply the reacted sample and reagents and for adetection region for reading the test results. Fiduciary markers, areference color scale, and a barcode that identifies the test performedby the kit is found in the housing. As the reacted sample and reagentsare moved along the lateral flow assay test strip to the detectionregion, the detection moiety from the cleaved single stranded detectornucleic acid are bound to a capture molecule on the support medium and adetection molecule in a detection region to generate a detectable signalon the support medium. The detectable signal is shown as a line in thedetection region of the support medium. Once the test is completed, aline for a positive control marker and another line for a positive testare visible through the detection region opening.

After a predetermined amount of time after applying the reacted sampleand reagents to the support medium, a mobile device to obtain the testresults is used by the individual. A mobile application for reading ofthe test results on a mobile device with a camera is opened by theindividual and an image of the support medium is taken, including thedetection region, barcode, reference color scale, and fiduciary markerson the housing, using the camera of the mobile device and the GUI of themobile application. The test based on the barcode in the image isidentified by the mobile application, the detection region in the imagewith the fiduciary markers and a reference color scale on the housing inthe same image is analyzed based on the identification of the test withthe barcode, and the presence or absence of the bacteria or the virusresponsible for a communicable disease is determined. The results of thetest are presented to the individual by the mobile application. The testresults are stored in the mobile application. A remote device is used tocommunicate with the mobile application and the data of the test resultsis transferred to the remote device. The test results are viewedremotely from the remote device by another individual, such as ahealthcare professional.

Example 2 Testing of One Communicable Disease—Dipstick Method

A biological sample from an individual is tested to determine whetherthe individual has a communicable disease. The biological sample istested to detect the presence or absence of a target nucleic acidindicative of a bacteria or a virus responsible for the communicabledisease.

A biological sample of urine is obtained from an individual and thebiological sample is applied to the reagents as described herein in areagent chamber provided in a kit. The reagents are comprised of a guidenucleic acid targeting a nucleic acid present in and specific to thebacteria or the virus, a programmable nuclease, and a single strandeddetector nucleic acid. In some examples, a CRISPR/Cas nuclease is usedas the programmable nuclease.

After the sample and the reagents are contacted for a predeterminedtime, one end of a support medium is placed into the reagent chamber byan individual to apply the reacted sample and reagents to a sample padregion on the support medium. The support medium is comprised of alateral flow assay test strip. As the reacted sample and reagents aremoved along the test strip to the detection region, a line for apositive control marker is observed (e.g. is visible) in the detectionregion. After a predetermined amount of time after applying the reactedsample and reagents to the support medium, the support medium is placedinto a protective housing with an opening for the detection region forreading the test results, fiduciary markers, a reference color scale,and a barcode that identifies the test performed by the kit.

A mobile device is used to obtain the test results. A mobile applicationfor reading of the test results on a mobile device with a camera isopened and an image of the support medium is taken, including thedetection region, barcode, reference color scale, and fiduciary markerson the housing, using the camera of the mobile device and the mobileapplication. The test based on the barcode in the image is identified bythe mobile application, the detection region in the image with thefiduciary markers and a reference color scale is analyzed on the housingin the same image based on the identification of the test with thebarcode, and the presence or absence of the bacteria or the virusresponsible for a communicable disease is determined. The results of thetest are presented to the individual by the mobile application. The testresults are stored in the mobile application. A remote device is used tocommunicate with the mobile application and the data of the test resultsis transferred to the remote device. The test results are viewedremotely from the remote device by another individual, such as ahealthcare professional.

Example 3 Testing of One Communicable Disease—In Situ Cleaving onSupport Medium

A biological sample from an individual is tested to determine whetherthe individual has a communicable disease. The biological sample istested to detect the presence or absence of a target nucleic acidindicative of a bacteria or a virus responsible for the communicabledisease.

A biological sample of urine is obtained by an individual and thebiological sample is applied to the reagents described herein on asample pad region on a support medium provided in a kit. The reagentsare comprised of a guide nucleic acid targeting a nucleic acid presentin and specific to the bacteria or the virus, a programmable nuclease,and a single stranded detector nucleic acid. The support medium iscomprised of a lateral flow assay test strip encased in a protectivehousing with an opening for the detection region for reading the testresults, fiduciary markers, a reference color scale, and a barcode thatidentifies the test performed by the kit.

After the sample and the reagents are contacted for a predetermined timeon the support medium, the reacted sample and reagents are moved alongthe support medium to a detection region on the support medium.Optionally, a small volume of buffer is placed is used to help move thereacted sample and reagents to the detection region. As the reactedsample and reagents are moved along the test strip to the detectionregion, a line for a positive control marker is observed (e.g., isvisible) in the detection region.

A mobile device is used to obtain the test results. The test based onthe barcode in the image is identified by a mobile application on themobile device, the detection region in the image is analyzed, and thepresence or absence of the bacteria or the virus responsible for acommunicable disease is determined. The results of the test arepresented to the individual by the mobile application. The test resultsare stored in the mobile application. A remote device is used tocommunicate with the mobile application and the data of the test resultsis transferred to the remote device. The test results are viewedremotely from the remote device by another individual, such as ahealthcare professional.

Example 4 Testing of Multiple Communicable Diseases—Multiple LateralFlow Assay

A biological sample from an individual is tested to determine whetherthe individual has one or more communicable diseases. The biologicalsample is tested to detect the presence or absence of one or more oftarget nucleic acids, where the individual target nucleic acid isindicative of a bacteria or a virus responsible for one of thecommunicable diseases.

A biological sample of urine is obtained and the biological sample isapplied to multiple reagent chambers provided in a kit to test for apanel of communicable diseases. Each reagent chamber is comprised of thereagents specific to detect one communicable disease. The reagents ineach reagent chamber is comprised of a guide nucleic acid targeting anucleic acid present in and specific to the bacteria or the virus; aprogrammable nuclease; and a single stranded detector nucleic acid.

After the sample and the reagents are contacted for a predeterminedtime, the reacted sample and reagents is applied from one of the reagentchambers to a matched sample pad region on a support medium. Eachreagent chamber is comprised of a matching sample pad region on thesupport medium. The support medium is comprised of multiple lateral flowassay test strips encased in a protective housing with openings for thematched sample pad regions to apply the reacted sample and reagents fromthe matching reagent chamber and for a detection region for reading thetest results. Fiduciary markers, a reference color scale, and a barcodethat identifies the tests performed by the kit are located in thehousing. As the reacted sample and reagents are moved along the lateralflow assay test strip to the detection region, a positive control markerfor each lateral flow test strip is observed (e.g., is visible) throughthe detection region opening.

After a predetermined amount of time after applying the reacted sampleand reagents to the support medium, a mobile device is used to obtainthe test results. A mobile application on the mobile device is used toidentify the test based on the barcode in the image, analyze thedetection region in the image, and determine the presence or absence ofthe bacteria or the virus responsible for a communicable disease. Theresults of the test are presented to the individual by the mobileapplication. The test results are stored in the mobile application. Aremote device is used to communicate with the mobile application and thedata of the test results is transferred to the remote device. The testresults are viewed remotely from the remote device by anotherindividual, such as a healthcare professional.

Example 5 Testing of Multiple Communicable Diseases—Multiplexed LateralFlow Assay

A biological sample from an individual is tested to determine whetherthe individual has one or more communicable diseases. The biologicalsample is tested to detect the presence or absence of one or more oftarget nucleic acids, where the individual target nucleic acid isindicative of a bacteria or a virus responsible for one of thecommunicable diseases.

A biological sample of urine is obtained and the biological sample isapplied to a reagent chamber provided in a kit to test for a panel ofcommunicable diseases. The reagent chamber is comprised of multiple setsof reagents to detect multiple communicable diseases. One set ofreagents to detect one communicable disease is comprised of a guidenucleic acid targeting a nucleic acid present in and specific to thebacteria or the virus for the communicable disease; a programmablenuclease; and a single stranded detector nucleic acid. Often, thecommunicable disease is identified as sepsis.

After the sample and the reagents are contacted for a predeterminedtime, the reacted sample and reagents are applied to a sample pad regionon a support medium. The support medium is comprised of a multiplexedlateral flow assay test strip that detects multiple detector moleculeson the test strip. The lateral flow assay strip is encased in aprotective housing with openings for the sample pad region to apply thereacted sample and reagents and for a detection region for reading thetest results. Fiduciary markers, a reference color scale, and a barcodethat identifies the tests performed by the kit are also located in thehousing. As the reacted sample and reagents are moved along the lateralflow assay test strip to the detection region, a positive control markerfor each lateral flow test strip is observed (e.g., is visible) throughthe detection region opening.

After a predetermined amount of time after applying the reacted sampleand reagents to the support medium, a mobile device is used to obtainthe test results. A mobile application on the mobile device is used toidentify the test based on the barcode in the image, analyze thedetection region in the image, and determine the presence or absence ofthe bacteria or the virus responsible for a communicable disease. Theresults of the test are presented to the individual by the mobileapplication. The test results are stored in the mobile application. Aremote device is used to communicate with the mobile application and thedata of the test results is transferred to the remote device. The testresults are viewed remotely from the remote device by anotherindividual, such as a healthcare professional.

Example 6 Testing of RNA Reporter Molecules in an Lbucas13a Assay

The fluorescence of RNA reporter molecules were tested for use withLbuCas13 assays. The reporter molecules tested were FAM-UU:/56-FAM/TTrUrUTT(SEQ ID NO: 5)/3IABkFQ/; FAM-UU-long:56-FAM/TTTTrUrUTTTT(SEQ ID NO: 4)/3IABkFQ/; FAM-AU: /56-FAM/TArArUGC(SEQID NO: 6)/3IABkFQ/; FAM-UG: /56-FAM/TArUrGGC(SEQ ID NO: 7)/3IABkFQ/;FAM-U10: /56-FAM/rUrUrUrUrUrUrUrUrUrU(SEQ ID NO: 3)/3IABkFQ/; FAM-U5:/56-FAM/rUrUrUrUrU(SEQ ID NO: 1)/3IABkFQ/; FAM-U8:/56-FAM/rUrUrUrUrUrUrUrU(SEQ ID NO: 2)/3IABkFQ/; and RNAse Alert:Proprietary reporter from Integrated DNA Technologies RNaseAlertSubstrate Nuclease Detection System. 56-FAM is 5′ 6-Fluorescein dye thatemits light at about 520 nm and 3IABkFQ is 3′Iowa Black FQ, which is aquencher for use with fluoroscein and other fluorescent dyes that emitin the green to pink spectral range. Each reporter was tested, from leftto right, with no enzyme (no LbuCas13a), with RNAse A, with LbuCas13abut without a target nucleic acid; or with LbuCas13a and with the targetnucleic acid, as shown in FIG. 1 . When tested with no enzyme (negativecontrol), all reporters showed little to no relative fluorescence. Whentested with RNAse A (positive control), all reporters exhibited highfluorescence. When tested with LbuCas13a without a target nucleic acid(inactive LbuCas13a), the “best” reporters generated very littlefluorescence, such as the FAM-U5 and FAM-UU-long reporters. The RNAseAlert, which is the current standard reporter, showed significantfluorescence. When tested with LbuCas13a with a target nucleic acid(active LbuCas13a), the “best” reporters generated high fluorescence,such as the U5 and UU-long reporters.

Example 7

Mixing CRISPR RNAs (crRNAs) in a Single Reaction Allowed Detection ofTwo Species' RNA Simultaneously

The fluorescent signal of samples with crRNAs from two species fordetection of RNA was tested. In this assay, the fluorescent signal ofsamples with various combinations of no RNA, RNA from E. coli only, RNAfrom Chlamydia only, or RNA from both Chlamydia and E. coli mixed withCRISPR RNAs (crRNAs) for the Chlamydia RNA, crRNAs for the E. coli RNA,or crRNAs for Chlamydia RNA mixed with crRNAs for E. coli RNA wasassessed as shown in FIG. 2 .

The mixed crRNAs of crRNAs for E. coli RNA and crRNAs for Chlamydia RNAproduced fluorescent signal in samples comprising RNA from E. coli mixedwith RNA from Chlamydia; RNA from E. coli only; or RNA from Chlamydiaonly. The RNA from E. coli mixed with RNA from Chlamydia producedfluorescent signal in samples comprising crRNAs for E. coli RNA mixedwith crRNAs for Chlamydia RNA; crRNAs for E. coli RNA only; or crRNAsfor Chlamydia RNA only. crRNAs for Chlamydia RNA produced fluorescentsignal in the sample comprising RNA from Chlamydia. crRNA for E. coliRNA produced fluorescent signal in the sample comprising E. coli RNA.The individual crRNAs did not produce fluorescent when mixed with thenon-matching target RNA or with no RNA. All the assay samples alsocomprised Cas13a.

Example 8 Mixing Multiple crRNAs Against the Same Gene or SpeciesIncreases Fluorescent Signal

The fluorescent signal of samples with different crRNAs for detection ofRNA was tested. The fluorescent signal for three different crRNAs eitherindividually or as a mixture of all three crRNAs, with either no RNA(dark bars; 0.0 nM RNA) or a target RNA with sites for all three crRNAs(light bars; 0.001 nM RNA) was detected as shown in FIG. 3 .

The mixing of all three crRNAs produced more signal than a single crRNAof each of the three different crRNAs. Therefore, mixing differentcrRNAs may be a strategy to increase fluorescent signal of an assay, andthus increase assay sensitivity.

Example 9 Autofluorescent Signal in Urine at Various Wavelengths

The autofluorescent signal in human urine was tested at differentwavelengths associated with different fluorophores as shown in FIG. 4 .Human urine has increased autofluorescence in the wavelengths associatedwith detection of FAM-based reporter molecules, whereas theautofluorescence of urine was not as prevalent in the wavelengthsassociated with detection of AlexaFluor594, ATTO633, TYE665, or IRDYE700fluorescent dyes.

Example 10 Use of RNAse Inhibitors for Cas13a Assays in Urine

The fluorescent signal in urine with different RNAse inhibitors wastested. The fluorescent signal in a urine fraction of 0 (buffer only;control) or a urine fraction of 0.18 (18% urine in buffer) with no RNAseinhibitor (left panel), with RibLock RNAse inhibitor (middle panel), orwith polyvinyl sulfonic acid (PVS) (right panel) was detected as shownin FIG. 5A. Each of these conditions was tested with Cas13a, RNAreporter molecules, and either 0.0 nM target RNA or 0.09 nM target RNA.

In the urine fraction of 0 tested without RNAse inhibitor (left panel ofFIG. 5A), the fluorescent signal was produced only in the presence oftarget RNA, indicating the Cas13 assay works in buffer. However, in theurine fraction of 0.18 without RNAse inhibitor (left panel of FIG. 5A),the sample without the target RNA had high fluorescent signal. This wasmost likely due to nonspecific RNAses in body fluids/urine cleaving theRNA reporter molecules despite lack of activation of Cas13a. Asexpected, in the urine fraction of 0.18 without RNAse inhibitor and withthe target RNA had high fluorescent signal. * Indicate data was cut-off.FIG. 5B shows the rescaled y-axis for the left panel of FIG. 5A, whichthe y-axis Fluorescence (AU) was rescaled from 0 to 3000 at intervals of500 in FIG. 5A to 0 to 12000 at intervals of 2000 in FIG. 5B.

In the urine fraction of 0 tested with RiboLock RNAse inhibitor (middlepanel of FIG. 5A), the fluorescent signal was produced only in thepresence of target RNA, indicating Cas13a can cleave RNA reportermolecules in the presence of RiboLock RNAse inhibitor. In the urinefraction of 0.18 tested with RiboLock RNAse inhibitor, the fluorescentsignal was produced only in the presence of the target RNA, indicatingthat the RiboLock RNAse inhibitor inhibited the endogenous RNAses in theurine.

In the urine fraction of 0 tested with polyvinyl sulfonic acid (PVS)(right panel of FIG. 5A), the fluorescent signal was not produced in thepresence of target RNA, indicating Cas13a cleaving RNA reportermolecules was inhibited by the PVS. Furthermore, in the urine fractionof 0.18 tested with PVS, the fluorescent signal, although present, wassimilar between the samples with or without the target RNA, indicatingthat the PVS partially inhibited the endogenous RNAses in the urine, butalso inhibited the Cas13a cleaving of RNA reporter molecules.

Example 11 Fluorophore Fluorescent Signal in Urine

The fluorescent signal of different fluorophores in urine was tested.FAM, AlexaFluor594, ATTO633, TYE665, and IRDYE700 fluorophores in humanurine either with or without RNAse inhibitors was tested. A ratio offluorescence for the fluorescent signal of the each fluorophore eitherwith or without RNAse inhibitors was used to create the ratio offluorescence for each fluorophore, which was then normalized to ratio offluorescence for the FAM fluorophore as is shown in FIG. 6 .

Example 12 Comparisons of Different Fluorescent Reporter Molecules withDifferent Buffers

The fluorescent signal of FAM, TYE665, and IRDYE700 reporter moleculeswas compared in the original Cas13a buffer (20 mM HEPES pH 6.8, 50 mMKCl, 5 mM MgCl₂, and 5% glycerol) versus in an enhanced buffer(MBuffer1; comprising 100 mM Imidazole pH 7.5; 250 mM KCl, 25 mM MgCl₂,50 ug/mL BSA, 0.05% Igepal Ca-630, and 25% Glycerol). Furthermore, thereporter performance was evaluated in the standard Cas13a detectionassay (original buffer) with 100 fM target RNA (FIG. 7A) or in urinewith 10 pM target RNA (FIG. 7B).

As shown in FIG. 7A, the background subtracted fluorescent signal of RNAreporter molecules with Cas13a and 100 fM of target RNA in either theoriginal Cas13a buffer or an enhanced buffer (MBuffer1) was detected.

As shown in FIG. 7B, the background subtracted fluorescent signal of RNAreporter molecules with Cas13a and 10 pM of target RNA in either theoriginal Cas13a buffer or an enhanced buffer (MBuffer1) was detected.

For FIG. 7A and FIG. 7B, FAM-U5 is/56-FAM/rUrUrUrUrU(SEQ ID NO:1)/3IABkFQ/; TYE665-U5 is/5TYE665/rUrUrUrUrU(SEQ ID NO: 1)/3IAbRQSp/;and IRDYE700-U5 is/5IRD700/rUrUrUrUrU(SEQ ID NO: 1)/3IRQC1N/. In thesereporter molecules, rU indicates a uracil ribonucleotide; 56-FAMindicates 5′ 6-Fluorescein dye; 3IABkFQ indicates 3′ Iowa Black FQ;5TYE665 indicates 5′ TYE 665; 3IAbRQsp indicates 3′ Iowa Black RQ;5IRD700 indicates 5′ IRDye 700; and 3IRQClN indicates IRDye QC-1quencher.

Example 13 Testing of Chlamydia Infection—In Situ Cleaving on SupportMedium

A biological sample from an individual is tested to determine whetherthe individual has a Chlamydia infection. The biological sample istested to detect the presence or absence of a target nucleic acidcomprising GAGTATGGGAGAGTAGGTCG (SEQ ID NO: 168) indicative of thepresence of Chlamydia infection.

A biological sample of urine is obtained and the biological sample isapplied to the reagents described herein on a sample pad region on asupport medium provided in a kit. The reagents are comprised of a guidenucleic acid targeting a nucleic acid present in and specific toChlamydia, a programmable nuclease LbuCas13a, and a single strandeddetector nucleic acid. The support medium is comprised of a lateral flowassay test strip encased in a protective housing with an opening for thedetection region for reading the test results, fiduciary markers, areference color scale, and a barcode that identifies the test performedby the kit.

After the sample and the reagents are contacted for a period of timeranging from 5 minutes to 120 minutes on the support medium, the reactedsample and reagents are moved along the support medium to a detectionregion on the support medium. Optionally, a small volume of buffer isused to help move the reacted sample and reagents to the detectionregion. As the reacted sample and reagents are moved along the teststrip to the detection region, a line for a positive control marker isobserved (e.g., is visible) in the detection region.

A mobile device is used to obtain the test results. A mobile applicationof the mobile device is used to identify the test based on the barcodein the image, analyze the detection region in the image, and determinethe presence or absence of the target nucleic acid indicative ofChlamydia infection. The test results are viewed by the individual. Thetest results are stored in the mobile application. A remote device isused to communicate with the mobile application and the data of the testresults is transferred to the remote device. The test results are viewedremotely from the remote device by another individual, such as ahealthcare professional.

Example 14 Testing of Gonorrhea Infection—In Situ Cleaving on SupportMedium

A biological sample from an individual is tested to determine whetherthe individual has a Gonorrhea infection. The biological sample istested to detect the presence or absence of a target nucleic acidindicative of the presence of Gonorrhea infection.

A biological sample of urine is obtained and the biological sample isapplied to the reagents described herein on a sample pad region on asupport medium provided in a kit. The reagents are comprised of a guidenucleic acid targeting a nucleic acid present in and specific toGonorrhea, a programmable nuclease LbuCas13a, and a single strandeddetector nucleic acid. The support medium is comprised of a lateral flowassay test strip encased in a protective housing with an opening for thedetection region for reading the test results, fiduciary markers, areference color scale, and a barcode that identifies the test performedby the kit.

After the sample and the reagents are contacted for a period of timeranging from 5 minutes to 120 minutes on the support medium, the reactedsample and reagents are moved along the support medium to a detectionregion on the support medium. Optionally, a small volume of buffer isused to help move the reacted sample and reagents to the detectionregion. As the reacted sample and reagents are moved along the teststrip to the detection region, a line for a positive control marker isobserved (e.g., is visible) in the detection region.

A mobile device is used to obtain the test results. A mobile applicationof the mobile device is used to identify the test based on the barcodein the image, analyze the detection region in the image, and determinethe presence or absence of the target nucleic acid indicative ofGonorrhea infection. The test results are viewed by the individual. Thetest results are stored in the mobile application. A remote device isused to communicate with the mobile application and the data of the testresults is transferred to the remote device. The test results are viewedremotely from the remote device by another individual, such as ahealthcare professional.

Example 15 Testing of Chlamydia Infection and GonorrheaInfection—Multiple Lateral Flow Assay

A biological sample from an individual is tested to determine whetherthe individual has Chlamydia and Gonorrhea. The biological sample istested to detect the presence or absence of one or more of targetnucleic acids, where the individual target nucleic acid is indicative ofa Chlamydia infection or a Gonorrhea infection.

A biological sample of urine is obtained and the biological sample isapplied to two reagent chambers provided in a kit to test for Chlamydiaand Gonorrhea. Each reagent chamber is comprised of the reagentsspecific to detect either Chlamydia or Gonorrhea. The reagents in eachreagent chamber is comprised of a guide nucleic acid targeting a nucleicacid present in and specific to either Chlamydia or Gonorrhea; aprogrammable nuclease; and a single stranded detector nucleic acid.

After the sample and the reagents are contacted for a period of timeranging from 5 minutes to 120 minutes, the reacted sample and reagentsfrom one of the reagent chambers is applied to a matched sample padregion on a support medium. Each reagent chamber has a matching samplepad region on the support medium. The support medium is comprised ofmultiple lateral flow assay test strips encased in a protective housingwith openings for the matched sample pad regions to apply the reactedsample and reagents from the matching reagent chamber and for adetection region for reading the test results. Fiduciary markers, areference color scale, and a barcode that identifies the tests performedby the kit are located in the housing. As the reacted sample andreagents are moved along the lateral flow assay test strip to thedetection region, a positive control marker for each lateral flow teststrip is observed (e.g., is visible) through the detection regionopening.

After a period of time ranging from 1 minute to 120 minutes afterapplying the reacted sample and reagents to the support medium, a mobiledevice is used to obtain the test results. A mobile application of themobile device is used to identify the test based on the barcode in theimage, analyze the detection region in the image, and determine thepresence or absence of the target nucleic acid indicative of Chlamydiainfection or Gonorrhea infection. The test results are viewed by theindividual. The test results are stored in the mobile application. Aremote device is used to communicate with the mobile application and thedata of the test results is transferred to the remote device. The testresults are viewed remotely from the remote device by anotherindividual, such as a healthcare professional.

Example 16 Testing of Chlamydia Infection and GonorrheaInfection—Multiplexed Lateral Flow Assay

A biological sample from an individual is tested to determine whetherthe individual has Chlamydia or Gonorrhea. The biological sample istested to detect the presence or absence of one or more of targetnucleic acids, where the individual target nucleic acid is indicative ofa Chlamydia infection or Gonorrhea infection.

A biological sample of urine is obtained and the biological sample isapplied to a reagent chamber provided in a kit to test for Chlamydiainfection and Gonorrhea infection. The reagents chamber is comprises odreagents sets to detect either Chlamydia or Gonorrhea. One set ofreagents to detect Chlamydia is comprised of a guide nucleic acidtargeting a nucleic acid present in and specific to a Chlamydiainfection; a first programmable nuclease, LbuCas13a; and at least onepopulation of a first single stranded detector nucleic acid. A secondset of reagents to detect Gonorrhea is comprised of a guide nucleic acidtargeting a nucleic acid present in and specific to a Gonorrheainfection; a second programmable nuclease, LbaCas13a; and at least onepopulation of a second single stranded detector nucleic acid.

After the sample and the reagents are contacted for a period of timeranging from 5 minutes to 120 minutes, the reacted sample and reagentsare applied to a sample pad region on a support medium. The supportmedium is comprised of a multiplexed lateral flow assay test strip thatcan detect the at least one population of first single stranded detectornucleic acid and the at least one population of second single strandeddetector nucleic acid on the test strip. The lateral flow assay strip isencased in a protective housing with openings for the sample pad regionto apply the reacted sample and reagents and for a detection region forreading the test results. Fiduciary markers, a reference color scale,and a barcode that identifies the tests performed by the kit are locatedin the housing. As the reacted sample and reagents are moved along thelateral flow assay test strip to the detection region, a positivecontrol marker for each lateral flow test strip is observed (e.g., isvisible) through the detection region opening.

After a period of time ranging from 1 minute to 120 minutes afterapplying the reacted sample and reagents to the support medium a mobiledevice is used to obtain the test results. A mobile application of themobile device is used to identify the test based on the barcode in theimage, analyze the detection region in the image, and determine thepresence or absence of a Chlamydia infection and a Gonorrhea infection.The test results are viewed by the individual. The test results arestored in the mobile application. A remote device is used to communicatewith the mobile application and the data of the test results istransferred to the remote device. The test results are viewed remotelyfrom the remote device by another individual, such as a healthcareprofessional.

Example 17 Testing of Cancer Gene—In Situ Cleaving on Support Medium

A biological sample from an individual is tested to determine whetherthe individual has a cancer associated with the expression of a specificgene, such as EGFR, T2ERG, PCA3, or PSA. The biological sample is testedto detect the presence or absence of a target nucleic acid indicative ofthe presence of the expression of the cancer gene. Blood, plasma, cfDNA,liquid biopsy, or urine is used as the biological sample. For example,for EGFR detection, a blood sample is obtained for testing. For T2ERG,PCA3, or PSA, a urine sample is obtained for testing.

A biological sample is obtained and the biological sample is applied tothe reagents described herein on a sample pad region on a support mediumprovided in a kit. The reagents are comprised of a guide nucleic acidtargeting a cancer gene such as EGFR, T2ERG, PCA3, or PSA, aprogrammable nuclease such as a Cas12 or Cas14 protein, and a singlestranded detector nucleic acid. The support medium is comprised of alateral flow assay test strip encased in a protective housing with anopening for the detection region for reading the test results, fiduciarymarkers, a reference color scale, and a barcode that identifies the testperformed by the kit.

After the sample and the reagents are contacted for a period of timeranging from 5 minutes to 120 minutes on the support medium, the reactedsample and reagents are moved along the support medium to a detectionregion on the support medium. Optionally, a small volume of buffer isused to help move the reacted sample and reagents to the detectionregion. As the reacted sample and reagents are moved along the teststrip to the detection region, a line for a positive control marker isobserved (e.g., is visible) in the detection region.

A mobile device is used to obtain the test results. A mobile applicationof the mobile device is used to identify the test based on the barcodein the image, analyze the detection region in the image, and determinethe presence or absence of the target nucleic acid indicative ofexpression of the cancer gene. The test results are viewed by theindividual. The test results are stored in the mobile application. Aremote device is used to communicate with the mobile application and thedata of the test results is transferred to the remote device. The testresults are viewed remotely from the remote device by anotherindividual, such as a healthcare professional.

Example 18 Testing of Genetic Disorder—In Situ Cleaving on SupportMedium

A biological sample from an individual is tested to determine whetherthe individual has a genetic disorder, such as cystic fibrosis or celiacdisease, based on the expression of a specific gene. The biologicalsample is saliva and is tested to detect the presence or absence of atarget nucleic acid indicative of the presence of the expression of thegene associated with the genetic disorder.

A biological sample of saliva is obtained and the biological sample isapplied to the reagents described herein on a sample pad region on asupport medium provided in a kit. The reagents are comprised of a guidenucleic acid targeting a gene associated with a genetic disorder, aprogrammable nuclease such as LbaCas12a protein or a Cas14 protein, anda single stranded detector nucleic acid. The support medium is comprisedof a lateral flow assay test strip encased in a protective housing withan opening for the detection region for reading the test results,fiduciary markers, a reference color scale, and a barcode thatidentifies the test performed by the kit.

After the sample and the reagents are contacted for a period of timeranging from 5 minutes to 120 minutes on the support medium, the reactedsample and reagents are moved along the support medium to a detectionregion on the support medium. Optionally, a small volume of buffer isused to help move the reacted sample and reagents to the detectionregion. As the reacted sample and reagents are moved along the teststrip to the detection region, a line for a positive control marker isobserved (e.g., is visible) in the detection region.

A mobile device is used to obtain the test results. A mobile applicationof the mobile device is used to identify the test based on the barcodein the image, analyze the detection region in the image, and determinethe presence or absence of the target nucleic acid indicative ofexpression of the gene associated with the genetic disorder. The testresults are viewed by the individual. The test results are stored in themobile application. A remote device is used to communicate with themobile application and the data of the test results is transferred tothe remote device. The test results are viewed remotely from the remotedevice by another individual, such as a healthcare professional.

Example 19 Detection of a Single Nucleotide Polymorphism (SNP) VersusWild-Type (WT) in P. falciparum

This example shows that Cas12a can be used to detect a single nucleotidepolymorphism (SNP) versus wild-type (WT) allele in P. falciparum.Kelch13 mutants in P. falciparum are associated with Artemisininresistance.

Cas12a is used for detection of a WT allele of kelch13 versus detectionof a C580Y allele of kelch13. FIG. 8A is a schematic showing a guidenucleic acid (gRNA) for detection of a WT allele of kelch13, and a gRNAfor detection of a C580Y allele of kelch13. The gRNA for detection of aWT allele of kelch13 binds to the WT allele of kelch13, but does notbind to the kelch13 C580Y allele. The gRNA for detection of the kelch13C580Y allele binds to the kelch13 C580Y allele, but does not bind to thekelch13 WT allele.

FIG. 8B shows Cas12a detected WT kelch13 versus a kelch13 SNPresponsible for Artemisinin resistance in P. falciparum. For the WTkelch13, the WT kelch13 gRNA (WT gRNA) produced fluorescence in thepresence of the WT kelch13 target nucleic acid molecule (WT target) butnot in the presence of the target kelch13 nucleic acid moleculecomprising the SNP (mut target). For the kelch13 SNP, the kelch13 SNPgRNA (mut gRNA) produced fluorescence in the presence of the targetkelch13 nucleic acid molecule comprising the SNP (mut target), but notin the presence of the WT target. Therefore, Cas12a detected a SNPversus WT allele.

Example 20 Detection of a Single Nucleotide Polymorphism (SNP) VersusWild-Type (WT) in N. Gonorrhea

This example shows that Cas12a can be used to detect a single nucleotidepolymorphism (SNP) versus wild-type (WT) allele in N. gonorrhea. A SNPmutant allele in N. gonorrhea is associated with azithromycinresistance.

FIG. 8C shows species-specific detection of 16S of N. gonorrhea by Cas13using a reporter molecule (/5-6FAM/rUrUrUrUrU(SEQ ID NO: 1)/3IABkFQ/)and detection of an azithromycin resistance SNP for N. gonorrhea (23Smutant) versus wild-type (23S WT) N. gonorrhea by Cas12 using a reportermolecule (/AF594/TTATTATT/3IAbRQSp/), all in a single reaction. The topgrid shows detection of N. gonorrhea using a Cas13 species-specific 16SgRNA and detection of WT 23S using a Cas12 gRNA targeting the 23S WT,indicating the N. gonorrhea is susceptible to antibiotic treatment usingazithromycin. The bottom grid shows detection of N. gonorrhea using aCas13 species-specific 16S gRNA and detection of mutant 23S using aCas12 gRNA targeting the 23S mutant, indicating the N. gonorrhea isresistant to antibiotic treatment using azithromycin.

Example 21 Detection of a Nucleic Acid Using a Fluidic Device

This example illustrates detection of a nucleic acid using programmablenuclease in a fluidic device. In some examples, a CRISPR/Cas nuclease isused as the programmable nuclease, and a CRISPR-Cas reaction fordetection of a target nucleic acid in a sample is carried out using afluidic device.

FIG. 9 shows a schematic illustrating a workflow of the CRISPR-Casreaction. Step 1 in the workflow is sample preparation, Step 2 in theworkflow is nucleic acid amplification. Step 3 in the workflow is Casreaction incubation. Step 4 in the workflow is detection (readout).Steps 1 and 2 are optional, and steps 3 and 4 can occur concurrently, ifdetection and readout are incorporated to the Cas reaction. FIG. 10shows a fluidic device for sample preparation that is used. The samplepreparation fluidic device processes different types of biologicalsample. The biological sample is finger-prick blood, urine or swabs withfecal, cheek or other collection. The sample is prepared in a fluidicdevice of FIG. 10 and is then introduced into a fluidic device.

The fluidic device is one of the three fluidic devices of FIG. 11 or thefluidic device of FIG. 13 . The three fluidic devices of FIG. 11 carryout a Cas reaction with a fluorescence or electrochemical readout. Anexploded view diagram summarizing the fluorescence and electrochemicalprocesses that are used for detection of the reaction are shown in FIG.12 . FIG. 12 shows schematic diagrams of a readout process that are usedincluding (a) fluorescence readout and (b) electrochemical readout. FIG.13 shows a fluidic device for coupled invertase/Cas reactions withcolorimetric or electrochemical/glucometer readout. This diagramillustrates a fluidic device for miniaturizing a Cas reaction coupledwith the enzyme invertase. Surface modification and readout processesare depicted in exploded view schemes at the bottom including (a)optical readout using DNS, or other compound and (b) electrochemicalreadout (electrochemical analyzer or glucometer).

A sample containing a target nucleic acid of interest is introduced intoa fluidic device of FIG. 10 . The sample is filtered and introduced intoa fluidic device of FIG. 11 or FIG. 13 , wherein the nucleic acid ofinterest is, optionally, amplified, and incubated with pre-complexed Casmix. The Cas-gRNA complex binds to its matching nucleic acid target fromthe amplified sample and is activated into a non-specific nuclease,which cleaves a nucleic acid-based reporter molecule to generate asignal readout. A target nucleic acid of interest is detected using afluorescence readout, an electrochemical readout, or anelectrochemiluminescence readout, as shown in FIG. 12 or an opticalreadout or electrochemical readout, as shown in FIG. 13 .

Example 22 Detection of Circulating RNA

This example illustrates a workflow for detection of circulating RNA inurine.

FIG. 14A shows diagram for the detection workflow of a target nucleicacid in sample of patient urine. First, RNA is extracted from the urinesample. Then the extracted urine undergoes a pre-amplification step inwhich the target nucleic acid is amplified. The amplicons are thencontacted to Cas13a complexed with a guide nucleic that binds to theamplicons, which initiates cleavage of a detector nucleic acidcomprising a fluorophore attached to a quencher by a nucleic acid. Uponcleavage of the detector nucleic acid, the fluorophore is detected as apositive signal, indicating the presence of the target nucleic acid inthe sample of patient urine.

Example 23 Detection of Prostate Cancer Biomarkers

This example shows prostate cancer biomarkers are detected using Cas13a.Additionally, this example illustrates that fluorescence output from thecleavage of detector nucleic acids by Cas13a is a linear function of theconcentration of the prostate cancer RNA biomarker for each of the threeRNA biomarkers tested.

FIG. 14B shows detection of prostate cancer RNA biomarkers using theworkflow of FIG. 14A, except the sample is from a prostate cell cancerline. The y-axis is background fluorescence (AU) and the x-axisindicates the detection of different prostate cancer RNA biomarkers(e.g., RNA #1, RNA #2, and RNA #3). Each RNA was detected in theprostate cancer cell line as indicated by the fluorescence. The sameworkflow and reagents were applied to a water sample and a samplecomprising RNA from a cervical cancer cell line, which were negativecontrols and showed little to no fluorescence indicating target nucleicacids encoding the prostate cancer RNA biomarkers were not present inthe samples as expected.

FIG. 14C shows that the fluorescence output as detected for eachprostate cancer RNA biomarker in FIG. 14B is a linear function of theconcentration of the target nucleic acid comprising encoding theprostate cancer RNA biomarker.

Example 24 HERC2 SNP Detection Using Cas12a

This example illustrates using Cas12a for detection of HERC2 SNPs.

FIG. 15 shows SNP detection using Cas12a with a blue-eye guide nucleicacid or a brown-eye guide nucleic acid in saliva samples from blue-eyedand brown-eyed individuals, which were spatially multiplexed.Amplification of the HERC2 gene from human genomic DNA was conducted byPCR for 20 minutes followed by incubation for 30 minutes with the guideRNA complexed with Cas12a in a 20 μl assay volume. Fluorescence wasdetected using a plate reader for each sample. Seven volunteer subjectswere tested. The brown eye allele of the HERC2 gene was detected in fourof the volunteers. The blue eye allele of HERC2 gene was detected infive of the volunteers. Volunteers with both brown and blue eye allelesdetected were heterozygotes of the HERC2 gene, but displayed thedominant brown eye color. Of the fourteen tests conducted on the sevenvolunteer samples, seven were found to true positive, seven were foundto be true negative, zero were found to be false positive, and zero werefound to be false negative.

Example 25 ALDH2 SNP Detection Using Cas12a

This example illustrates using Cas12a for detection of ALDH2 SNPs.

FIG. 16A illustrates that the workflow for the alcohol flush (ALDH2) SNPdetection. A saliva sample is taken from a subject and processed todetermine the genotype of the subject.

FIG. 16B shows alcohol flush (ALDH2) SNP detection using Cas12a with aguide nucleic acid for the G-SNP or a guide nucleic acid for the A-SNPin saliva samples from three volunteer subjects, which were spatiallymultiplexed. Amplification of the ALDH2 gene from human genomic DNA wasconducted by PCR followed by incubation with each guide RNA complexedwith Cas12a in 20 μl assay volumes. Fluorescence was detected using aplate reader for each sample. Both the G-SNP and A-SNP were detected inthe sample from volunteer #1. Only the G-SNP was detected in the samplesfrom volunteer #2 and volunteer #3.

FIG. 16C illustrates the genotype/phenotype correlation for the ALDH2SNP genotypes.

FIG. 16D shows the genotypes of each volunteer by sequencing, whichconfirms the genotype detected in FIG. 16B using Cas12a.

FIG. 16E is a table summarizing the parameters of FIG. 16B. TAT: turnaround time.

Example 26 Syndromic Panel Identification of Sepsis Using Cas12a

This example shows a potential panel of bacterial pathogens that can beused for identification of sepsis.

FIG. 17A shows the workflow for the exemplary syndromic panelidentification of sepsis of FIG. 17B. The workflow on the left shows aninput of mixed bacterial species that comprise the target nucleic acidsfor detection. DNA is extracted from these bacterial species, the targetDNA is amplified, and Cas12a complexed to guide RNAs for the targetnucleic acids for detection using spatial multiplexing. The binding ofthe target nucleic acids to the Cas12a complexed to guide RNAs for thetarget nucleic acids initiates cleavage of a detector nucleic acidcomprising a fluorophore attached to a quencher by a nucleic acid. Uponcleavage of the detector nucleic acid, the fluorophore is detected as apositive signal indicating the presence of the bacterial speciescomprising the target nucleic acids. The workflow on the right shows aninput of mixed bacterial species that lack the bacterial species fordetection. DNA is extracted from these bacterial species, the DNA isamplified and contacted to Cas12a complexed to guide RNAs for the targetnucleic acids for detection using spatial multiplexing. The lack ofbinding of target nucleic acids due to the absence of the target nucleicacids to the Cas12a complexed to guide RNAs for the target nucleic acidsdue to the absence of the target nucleic acids fails to initiatecleavage of a detector nucleic acid comprising a fluorophore attached toa quencher by a nucleic acid. Due to the lack of cleavage of thedetector nucleic acid, the fluorophore remains quenched in the intactdetector nucleic acid resulting in a negative signal indicating theabsence of bacterial species comprising the target nucleic acids.

FIG. 17B illustrates an exemplary test panel comprising 4 gram negative(top: Enterobacter cloacae, Klebsiella aerogenes, Proteus vulgaris, andSerratia marcesens) and 6 gram positive (after gram negative, top:Enterococcus faecalis, Enterococcus faecium, Staphylococcus aureus,Streptococcus intermedius, Streptococcus pneumoniae, and Streptococcuspyogenes) and bacterial pathogens from samples of purified genomic DNAbenchmarked to pre-blood culture concentrations that underwent theworkflow as shown on the right side of FIG. 17A. The extracted DNA wasamplified by PCR and incubated with guide RNA complexed with Cas12a in20 μl assay volumes, in which the guide RNA bind to the target nucleicacid from the bacterial pathogens. Fluorescence was detected using aplate reader for each sample. The right panel shows that fluorescencewas detected for each bacterial pathogen. The time to readout was 2.5hours.

Example 27 Cas13a and Cas12a Multiplexing in a One-Pot Reaction forSpecies Detection and Antibiotic Resistant Allele Detection

This example shows that a one-pot reaction with Cas13a and Cas12asuccessfully detects gonorrhea (species detected by Cas13a), and anantibiotic resistant allele (detected by Cas12a).

FIG. 18A shows Cas13 and Cas12 multiplexing for detection of a bacteria.Cas13 is used for species detection of the bacteria. Cas12 is used todetect a mutation in a locus of the bacteria that confers antibioticresistance.

FIG. 18B shows a one-pot Cas13a and Cas12a detection coupled withisothermal amplification for detection of gonorrhea. Nucleic acids froma gonorrhea sample were incubated with Cas13a complexed to guide RNAsfor the species (gonorrhea) target nucleic acid for detection of thebacteria species and were incubated with Cas12a complexed to guide RNAsfor the antibiotic resistance allele target nucleic acid for detectionof the antibiotic resistance allele, using multiplexing. The binding ofthe gonorrhea target nucleic acids to the Cas13a complexed to guide RNAsfor the species target nucleic acids initiated cleavage of a detectornucleic acid comprising a fluorophore attached to a quencher by anucleic acid. Upon cleavage of the detector nucleic acid, thefluorophore was detected as shown in the graph, indicating gonorrhea waspresent in the sample. Similarly, the binding of the antibioticresistance allele target nucleic acids to the Cas12a complexed to guideRNAs for the antibiotic resistance allele target nucleic acids initiatedcleavage of a detector nucleic acid comprising a fluorophore attached toa quencher by a nucleic acid. Upon cleavage of the detector nucleicacid, the fluorophore was detected as shown in the graph, indicating theantibiotic resistance allele was present in the sample. Samples withchlamydia and water were also tested using the same protocol, and asexpected, no fluorescence was detected for either sample.

Example 28 Detection of Chlamydia Using a Programmable Nuclease

This example shows that Chlamydia is detected in a sample byamplification paired with a programmable nuclease with similarsensitivity as qPCR. In some examples, a CRISPR/Cas nuclease is used asthe programmable nuclease.

FIG. 19A shows a comparison of detection for Chlamydia in 33 patientsamples using either qPCR or amplification paired with a CRISPR/Casnuclease to detect a Chlamydia target nucleic acid. Darker shadingindicates a stronger signal produced in response to the detection ofChlamydia target nucleic acids, while lighter shading indicates a weakersignal. Presence of Chlamydia target nucleic acid was measured usingqPCR (left) or detection with a programmable nuclease followingamplification (amp+CRISPR).

Example 29 Electrochemical Detection of Target Nucleic Acids Using aProgrammable Nuclease

This example describes electrochemical detection of target nucleic acidsusing a programmable nuclease system. Here, a programmable nucleasesystem was comprised of a DETECTR reaction using a CRISPR/Cas nuclease.In this assay a biotin-streptavidin signal enhancement method wasemployed using a biotinylated CRISPR-Cas reporter molecule, which iscleaved by the enzyme in the presence of a positive DETECTR reaction(one in which the target nucleic acid is present).

Other methods of electrochemical signal detection which may be used asan alternative to biotin-streptavidin electrochemical detection include(1) use of ferrocene-labelled oligos immobilized on the electrodesurface and (2) coupling of DETECTR to an invertase catalyzed reaction,also disclosed herein. The latter reaction will produce glucose that maybe detected with a glucometer directly, or indirectly. Electrochemicaldetection and detection using ferrocene-labelled oligos or usingbiotin-streptavidin are both potentiometric, while invertase catalyzedreactions are amperometric.

Described here are preliminary results, using a biotinylated reporterfor Cas12. The reporter was cleaved using a DNAse enzyme and cleavageresulted in a 21-μA increase in current at an −0.25V oxidation peakcompared to when the reporter was intact, demonstrating the use of anelectroactive CRISPR reporter in a DETECTR assay.

Results were collected using a benchtop, gold-standard electrochemicalanalyzer (uSTAT, Metrohm, USA). The sequence of the reporter was/5Biosg/TTTTTTTTTTTTTTTTTTTT/3MeBlN/(SEQ ID NO: 169). Signal wasdetected using a strip-based readout with an electroactive reporter.

The major advancements of this strip compared to existing commerciallyavailable strips was the introduction of this new type of CRISPR-Caselectroactive reporter molecule, which was tested in a proof-of-conceptassay by cleavage of the DNA reporter with a DNase. The new reportercomprised: (1) a 5′-Biotin moiety and (2) a 3′-methylene blue moiety.FIG. 20A shows a cyclic voltammogram showing potential (V) on the x-axisversus current (μA) on the y-axis for the reporter only versus a cleavedreporter. As shown in the graph, cleavage of the electroactive reporterled to increase in current. The experiment was run in the followingconditions: 100 μA sensitivity, 2 mV step, 50 mV amplitude, and 15 Hzfrequency. FIG. 20B shows a square wave voltammogram showing potential(V) on the x-axis versus current (μA) on the y-axis for the reporteronly versus a cleaved reporter. As shown in the graph, cleavage of theelectroactive reporter led to an increase in current. The experiment wasrun in the following conditions: 100 μA sensitivity, 50 mV step, 50 mVamplitude, 15 Hz frequency.

Example 30 Fluorescence-Based Device for Detection of Target NucleicAcids Using a Programmable Nuclease System

This example describes a fluorescence-based device for detection oftarget nucleic acids using a programmable nuclease system. Here, aprogrammable nuclease system was comprised of a DETECTR reaction using aCRISPR/Cas nuclease. Two approaches were used to develop a miniaturizeddevice for DETECTR reactions. First, a glass capillary (DrummondScientific, USA) was used as a single, capillarity driven vessel of theDETECTR reaction. Both flash-dried and liquid formulations of thereagents were used. Second, a commercially-available, plastic (TOPAS)microfluidic chip (Microfluidic Chip Shop, Germany) with no mechanicalactuation for mixing or reagent delivery was used.

Results were collected using (1) a portable, photodiode-basedfluorescence sensor (ESELog, Quiagen Lake Constance, Germany) and (2) acommercially-available transilluminator (E-GEL, Thermofisher, USA). Themajor advancement of the detection capabilities of this system includesthe first demonstration of an on-chip DETECR reaction.

FIG. 21A shows a graph of time in min on the x-axis versus fluorescence(AU) on the y-axis. The graph shows the real-time measurement offluorescence from a one-pot reverse transcription-recombinase polymeraseamplification-in vitro transcription (RT-RPA-IVT)-DETECTR reactioncarried out on chip. FIG. 21B shows images of the entire microfluidicchip used for the DETECTR reactions depicted in FIG. 21A under an E-GELtransilluminator. Shown at left is time 0 and shown at right is at timeof 35 min. The green bands at t=35 min are the two positive control(“PC”) reaction chambers. The negative control (“NC”) reaction chambersdo not show fluorescent bands. FIG. 21C shows a photograph of theprototype set-up (left image in figure) of the fluorescence-basedreadout for the on-chip, one-pot DETECTR reaction of this example. Thisphotograph shows an example of a breadboard prototype (top right imagein figure). The equipment used are off-the-shelf items including aplastic chip containing the DETECTR reagents from ChipShop made ofZeonor, an ESELog module that is an imager, and a heating componentusing ChipGenieP from ChipShop. The figure also shows a fluorescenceimage of eppendorph tubes containing the reaction at 30 minutes (bottomright image in figure).

Test reactions were performed by combining 40 nM crRNA and 40 nM Lbu-WTCas13a programmable nuclease in MBuffer1. The mixture was incubated at37° C. for 30 min. A reporter mixture comprising 170 nM reporter (e.g.,FAM-U5) and a murine RNase inhibitor (NEB). The crRNA-Cas13a-reportermixture was then (1) combined with 250 pM target nucleic acid and addedto the test chamber (positive control), or (2) added to the test chamberdirectly (negative control). Alternative methods were tested using 62.5nM crRNA an d 250 nM Lba-WT Cas12a or 62.5 nM crRNA an d 50 nM Lba-WTCas12a.

Example 31 Guide Pooling for High Sensitivity and Broad SpectrumDetection of Target Nucleic Acids

This example describes guide pooling for high sensitivity and broadspectrum detection of target nucleic acids. While traditional detectionrequires one guide RNA per target sequence/organism, the guide poolingmethods disclosed herein, including use of multiple gRNAs with one ormore CRISPR effector proteins, was found to be amenable for bothimproving sensitivity (in the case of guide tiling across a singletarget sequence/organism) and broad spectrum detection (in the case ofdetecting multiple target sequences/organisms in a single reaction).Thus, guide pooling was a useful method for enhancing detectionsensitivity performance as well as functioning as an initial triage stepthat is rapid and low-cost (e.g., an “alert” for blood-borne pathogens,pandemic flu, pan-bacterial detection, etc.) as compared to traditionaldiagnostic methods.

To perform DETECTR assay, a guide RNA (crRNA) was first complexed to theCas protein. The complexing reaction was carried out at 37° C. for 30minutes. Reporter and additional buffer were then added to complete thecomplex master mix. Finally, the complex was added to the samples todetect sequences specifically targeted by the guide. By pooling multipleguide RNAs designed to target difference sequences or different sequencesegments of the same target, it was possible to broaden the detectionspectrum in a single reaction and increase the detection efficiency. Toachieve this, guide RNAs were individually complexed to Cas protein athigh concentration. Multiple guide-protein complex reactions werepooled. After pooling, the reporter and addition buffer were added tocomplete the pooled complexes for use in the DETECTR assay.

A. Guide Pooling for Detection of Borrelia Strains.

Methods for guide pooling for detection of Borrelia strains involvedusing guide RNAs for 16S rRNA genes of different Borrelia strains. 19guide RNAs were designed to target 16S rRNA genes of the Borreliaspecies, B. burgdorferi, and/or B. mitamotoi. One guide RNA targets theRNase P RNA component H1 gene. TABLE 5 below lists the guide RNAs usedin this study.

TABLE 5 Guide RNA crRNA Sequence B. burgdorferi B. miyamotoi RNase PR0626 UAAUUUCUACUAAGUGUAGAUCCGG X AGCTTGGAACAGACTC (SEQ ID NO: 18) R0643UAAUUUCUACUAAGUGUAGAUAAGC X X UUCGCUUGUAGAUGAG (SEQ ID NO: 19) R0644UAAUUUCUACUAAGUGUAGAUACUU X GCAUGCUUAAGACGCA (SEQ ID NO: 20) R0645UAAUUUCUACUAAGUGUAGAUAUCC X UGGCUUAGAACUAACG (SEQ ID NO: 21) R0646UAAUUUCUACUAAGUGUAGAUAUUC X X GAUGAUACGCGAGGAA (SEQ ID NO: 22) R0647UAAUUUCUACUAAGUGUAGAUCAAC X AUAGGUCCACAGUUGA (SEQ ID NO: 23) R0648UAAUUUCUACUAAGUGUAGAUCAAC X AUAGUUCCACAGUUGA (SEQ ID NO: 24) R0649UAAUUUCUACUAAGUGUAGACAGC X AUAGUUCCACAGUUGA (SEQ ID NO: 25) R0650UAAUUUCUACUAAGUGUAGAUCAGC X X GUACACUACCAGGGUA (SEQ ID NO: 26) R0651UAAUUUCUACUAAGUGUAGAUCCCU X ACCAACUAGCUAAUAA (SEQ ID NO: 27) R0652UAAUUUCUACUAAGUGUAGAUCUAC X AAAGCUUAUUCCUCAU (SEQ ID NO: 28) R0653UAAUUUCUACUAAGUGUAGAUGGGU X CUAUAUACAGGUGCUG (SEQ ID NO: 29) R0654UAAUUUCUACUAAGUGUAGAUGGGU X CUGUAUACAGGUGCUG (SEQ ID NO: 30) R0655UAAUUUCUACUAAGUGUAGAUGUGA X X CUCAGCGUCAGUCUUG (SEQ ID NO: 31) R0656UAAUUUCUACUAAGUGUAGAUGUUA X ACACCAAGUGUGCAUC (SEQ ID NO: 32) R0657UAAUUUCUACUAAGUGUAGAUUAGG X AAAUGACAAAGCGAUG (SEQ ID NO: 33) R0658UAAUUUCUACUAAGUGUAGAUUCAU X X UUCCUACAAAGCUUAU (SEQ ID NO: 34) R0659UAAUUUCUACUAAGUGUAGAUUGCA X UAGACUUAUAUAUCCG (SEQ ID NO: 35) R0660UAAUUUCUACUAAGUGUAGAUAGGU X AUGUUUAGUGAGGGGG (SEQ ID NO: 36) R0661UAAUUUCUACUAAGUGUAGAUGUGA X GGGGGGUGAAGUCGUA (SEQ ID NO: 37)

The targets include double-stranded DNA gene fragments or PCR ampliconof gDNA. Borrelia targets include synthetic gene fragments of 16S RNAgenes of B. Burgdorferi and B. miyamotoi. Synthetic gene fragments werepurchased from a third-party vendor. The gene fragments were amplifiedin PCR reactions. The amplicons were purified and quantified. A total ofthree targets were obtained. The two B. burgdorferi gene fragments haveone base difference: B. miyamotoi 16S fragment, 1350 bp; B. burgdorferi16S fragment (guide 91 variant), 1607 bp; B. burgdorferi 16S fragment(guide 92 variant), 1670 bp. The RNase P target was amplified from humangDNA and the length of the amplicon was 101 bp.

The Cas protein used in these experiments was Lba-Cas12a. The reporterwas an 8-mer ssDNA with a FAM-labeled 5′ end and an Iowa BlackFQ-labeled 3′ end.

Guide RNA (crRNA) was individually complexed with Lba-Cas12a protein athigh concentration. Each crRNA was mixed at 3.2 uM with 3.2 uM ofLba-Cas12a in 1× MBuffer 2 (20 mM Tris HCl, pH8, 100 mM NaCl, 5 mMMgCl₂, 1 mM DTT, 5% glycerol, 50 ug/mL Heparin). The concentrations ofthe crRNA and protein were at least 4-fold higher than those in thestandard single guide complexing reaction. The mixture was incubated at37° C. for 30 minutes to form the guide-protein complex. TABLE 6 belowlists the formulation of the complexing reaction. The volumes are forone DETECTR reaction, and can be scaled up accordingly.

TABLE 6 Component Volume (μL) 5X MBuffer 2 1 crRNA (20 μM) 0.8Lba-Cas12a (5 μM) 3.2 TOTAL 5

Guide Pooling. At the completion of the incubation, guide pools weregenerated by combining equal volume of individual guide-proteincomplexing reactions. Several pools at different n-plex (n=number ofdifferent guides) levels were generated.

Pool1 combined an equal volume of all 19 Borrelia guide-proteincomplexing reactions and the RNase P guide-protein complexing reaction.This produced a 20-plex pool where the protein concentration is 3.2 pMand the concentration of each guide was 160 nM

Pool2 combined equal volume of 10 Borrelia guide-protein complexingreactions (R0643-R0652). This produced a 10-plex pool where the proteinconcentration was 3.2 pM and the concentration of each guide is 320 nM.Pool3 combined equal volume of 9 Borrelia guide-protein complexingreactions and the RNase P guide-protein complexing reaction(R0653-R0661, R0626). This produced a 10-plex pool where the proteinconcentration is 3.2 μM and the concentration of each guide was 320 nM.Pool4 combined equal volume of 5 Borrelia guide-protein complexingreactions and the RNase P guide-protein complexing reaction(R0643-R0647, R0626). This produced a 6-plex pool where the proteinconcentration is 3.2 μM and the concentration of each guide was 533 nM.Pool5 combined equal volume of 5 Borrelia guide-protein complexingreactions in pool4 without the RNase P guide-protein complexing reaction(R0643-R0647). This produced a 6-plex pool where the proteinconcentration is 3.2 μM and the concentration of each guide was 640 nM.Pool6 combined equal volume of 5 B. burgdorferi specific guide-proteincomplexing reactions and the RNase P guide-protein complexing reaction(R0645, R0647, R0659, R0660, R0661, R0626). This produced a 6-plex poolwhere the protein concentration is 3.2 pM and the concentration of eachguide was 533 nM. Pool7 was combined equal volume of 5 B. burgdorferispecific guide-protein complexing reactions in pool6 without the RNase Pguide-protein complexing reaction (R0645, R0647, R0659, R0660). Thisproduced a 5-plex pool where the protein concentration is 3.2 μM and theconcentration of each guide is 640 nM.

5 μl of the complexing reaction was used in each of the 20 μl DETECTRassays. The effective concentration in the assay of guides and proteinis one fourth of those in the complexing reactions.

Complex Master Mix. Complex Master Mixes of the guide pools werecompleted by adding equal volume of Mix2 (containing the ssDNA reporterand additional buffer, the formulation is listed in TABLE 7).

TABLE 7 Component Volume (μL) H2O 0.8 ssDNA reporter (10 uM) 0.2 5xMBuffer 2 3 Glycerol 80% 1 Total 5

Additionally, Mix2 was added to individual guide-protein complexingreaction to generate single guide complex master mix. In the complexmaster mix, the concentrations of the guides and proteins were dilutedin half.

DETECTR assay. The targets were diluted to 200 pM and 20 pM. In eachDETECTR assay, 10 μl of complex master mix was mixed with 10 ul ofsample in a well of a 384-well plate. The effective concentrations ofthe guides and protein were one fourth of those in the complexingreaction. The reaction was carried out in a TECAN Infinite 200 pro platereader at 37° C. The fluorescence raw data file was analyzed usinginternal software. The kinetics of the DETECTR assay was measured bymax_rate (estimated rate of cleavage of the reporter by the activatedCas protein). The activity of the guide pools versus the single guidewas measured against 200 pM targets (100 pM targets in the finalreaction. The max_rate of the DETECTR assay is summarized below in TABLE8.

TABLE 8 B.burgdorferi B.burgdorferi 16Sfrag 16Sfrag B.miyamotoi RowLabels (guide91var) (guide92var) 16Sfrag RNaseP8105 Pool1 20plex 13371326 1120 491 Pool2 10plex 1033 961 896 43 Pool3 10plex 939 1245 670 456Pool4 6plex 908 857 577 380 Pool5 5plex 851 851 497 22 Pool6 6plex 687649 25 425 Pool7 5plex 701 697 39 27 R0626 33 31 48 364 R0643 406 389409 29 R0644 285 252 168 29 R0645 336 339 40 38 R0646 294 318 274 34R0647 319 141 131 50 R0648 212 297 291 38 R0649 221 328 321 31 R0659 309310 32 25 R0660 442 414 29 41 R0661 189 183 38 34

The data showed that signals were clearly boosted by guide pooling. Thesignals of the 5/6-plex Pool 4, Pool5, Pool6, and Pool7 were two tothree times higher than a single guide assay. The signal increased asthe n-plex level was increased to 10- and 20-plex and the detectionsensitivity was improved from the single guide detection. The resultswere more evident for the B. miyamotoi detection. Pool6 and Pool7 had nomiyamotoi specific guides and generated no signals. As more miyamotoiguides are added to the guide pool, the signal for B. miyamotoi improvedto the levels of those for B. burgdorferi targets. The guide pools canbe adjusted to detect difference targets, B. burgdorferi only, B.burgdorferi plus B. miyamotoi, or B. burgdorferi plus B. miyamotoi plushuman RNase P. FIG. 23A shows a plate reader image of results summarizedin TABLE 8. FIG. 23B shows the plate layout corresponding to FIG. 23A.

The activities of the guide pools were also measured against 20 pMtargets (10 pM in the final reaction and the results are shown below inTABLE 9.

TABLE 9 B.burgdorferi B.burgdorferi Target coc 16Sfrag 16SfragB.miyamotoi Pool (10 pM) (guide91var) (guide92var) 16Sfrag Pool1 20plex100 2076 1686 1705 10 301 331 317 Pool2 10plex 10 200 225 253 Pool310plex 10 177 224 139

Results showed that the detection of 10 pM targets, which is near thedetection limit of the single guide assay, was improved and the poolingof the guides improved the sensitivity of the assay. FIG. 24A shows aplate reader image of a results summarized in TABLE 9. FIG. 24B showsthe plate layout corresponding to FIG. 24A.

B. Guide Pooling Top-Performing Individual gRNAs to Increase AssaySensitivity for Detection of RSV

Guide pooling was used to improve the detection limit of an assay forRSV detection. 33 guide RNAs for RSV guides were designed by tilingacross the target region. The guide RNAs were screened for activitiesand top performing guides were selected for pooling. RNA correspondingto the RSV target was generated from in vitro transcription (IVT)reaction. A Cas13a protein was used and the reporter was a 5-mer ssRNAwith a 5′ FAM and a 3′ Iowa Black FQ. FIG. 22A shows a panel of gRNAsfor RSV evaluated for detection efficiency. Darker squares in thebackground subtracted row indicate greater efficiency of detecting RSVtarget nucleic acids. FIG. 22B shows graphs of pools of gRNA versusbackground subtracted fluorescence. The left most graph shows pooling ofRSV gRNAs for detection of 4 pM of target nucleic acids. The middlegraph shows pooling of RSV gRNAs for detection of 800 fM of targetnucleic acids. The right most graph shows pooling of RSV gRNAs fordetection of 160 fM of target nucleic acids. gRNA sequences used in theRSV study are summarized below in TABLE 10.

TABLE 10 Guide name SEQ ID NO crRNA Sequence R0443 SEQ ID NO: 38GCCACCCCAAAAAUGAAGGGGACUA AAACAUCCUACAAAAAAAUGCUAAA R0444 SEQ ID NO: 39GCCACCCCAAAAAUGAAGGGGACUA AAACACCUACAAAAAAAUGCUAAAA R0445 SEQ ID NO: 40GCCACCCCAAAAAUGAAGGGGACUA AAACACUACAAAAAAAUGCUAAAAG R0449 SEQ ID NO: 41GCCACCCCAAAAAUGAAGGGGACUA AAACAAGAAACAUUUGAUAACAAUG R0450 SEQ ID NO: 42GCCACCCCAAAAAUGAAGGGGACUA AAACAGAAACAUUUGAUAACAAUGA R0452 SEQ ID NO: 43GCCACCCCAAAAAUGAAGGGGACUA AAACAAACAUUUGAUAACAAUGAAG R0453 SEQ ID NO: 44GCCACCCCAAAAAUGAAGGGGACUA AAACAACAUUUGAUAACAAUGAAGA R0456 SEQ ID NO: 45GCCACCCCAAAAAUGAAGGGGACUA AAACAUGCCUAUAACAAAUGAUCAG R0457 SEQ ID NO: 46GCCACCCCAAAAAUGAAGGGGACUA AAACAGCCUAUAACAAAUGAUCAGA

Example 32 Optimization of Temperature and Temperature Tolerance ofProgrammable Nucleases in Diagnostics

This example describes optimization of temperature and temperaturetolerance of a programmable nuclease for use in a diagnostic. Here,CRISPR-Cas proteins were used as the programmable nuclease, and theseCRISPR-Cas proteins were used in CRISPR diagnostics. The CRISPRdiagnostics of the present disclosure leverage the unique biochemicalproperties of Type V (e.g., Cas12) and Type VI (e.g., Cas13) CRISPR-Casproteins to enable the specific detection of nucleic acids. Theseproteins are directed to their target nucleic acid by a CRISPR RNA(crRNA), which is also known as a guide RNA (gRNA). Once bound to acomplementary target sequence, the Cas protein initiates indiscriminatecleavage of surrounding single-strand DNA or single-strand RNA. Whencoupled to a quenched fluorescence reporter or other cleavage reporter,fluorescent or other signal can be generated by the Cas protein only inthe presence of the target nucleic acid. CRISPR-Cas proteins have beenisolated from a variety of natural contexts and therefore have differenttolerances for elevated temperatures and optimal temperature ranges.These different tolerances for temperature can be used to activate orinhibit the proteins at different stages to allow for other molecularprocesses, such as target amplification, to occur.

Cas12M08 (a variant within the Cas12 family), Lba-Cas12a, and Cas13M26(Lbu-Cas13a) were incubated at 25° C., 30° C., 35° C., 40° C., 45° C.,and 50° C. with a target nucleic acid. Detection assays using thevarious Cas proteins were set up using 1 nM DNA target for Cas12proteins and 25 pM RNA target for Cas13a. The max_rate (fluorescenceunits/2 min) was determined for evaluating the efficiency of theproteins at various temperatures.

FIG. 25 shows that the functional range for the Type V protein Cas12M08is between 25° C. and 45° C., with maximal activity at 35° C. For theType V protein Lba-Cas12a the functional range is from 35° C. to 50° C.with peak activity around 40° C. For the Type VI protein Cas13M26(Lbu-Cas13a) the functional range is between 25° C. and 40° C. withmaximal activity between 30° C. and 35° C. Darker squares indicate ahigher max_rate and more efficient activity. As suggested in FIG. 25 ,it appears that Type V proteins, such as Cas12M08 and Lba-Cas12a, may bestable and functional at elevated temperatures. To test how stable eachof these proteins are, proteins were incubated for 15 minutes at 45° C.,50° C., 55° C., 60° C., 65° C., or 70° C. and then decreased thereaction temperature to 37° C.

FIG. 26 shows the results of incubating Cas12 proteins for 15 minutes at45° C., 50° C., 55° C., 60° C., 65° C., or 70° C. and then decreasingthe reaction temperature to 37° C. Lba-Cas12a was found to be functionaleven after incubation at 65° C. Cas12M08 was found to have no activitywhile at temperatures above 50° C., but after lowering the temperatureto 37° C., the enzymatic activity of the protein returned. Thistemperature shifting may be exploitable for use in isothermalamplification methods, where the amplification occurs at a highertemperature, but after lowering the reaction temperature the Cas proteincan be activated without compromising its functionality.

FIG. 27 shows that the stability of Cas12M08 at elevated temperatures isdependent on the buffer composition. Cas12M08 stability was assessedafter exposure to elevated temperatures for 30 minutes and then loweringthe reaction temperature to 37° C. A variety of buffers were tested todetermine their impact on the ability to turn Cas12M08 on and off basedon the reaction temperature. 0.5× NEBuffer4 (New England Biolabs)+0.05%TWEEN gave the best results, followed by 1× MBuffer3. 0.5× of IsothermalAmplification (IsoAmp) buffer (New England Biolabs) inhibited theCas12M08 reaction completely.

Example 33 Sample Preparation Protocol and Device Workflow

This example describes sample preparation protocol and device workflow.Collecting and processing material for diagnostic analysis is typicallyperformed at a point of care facility or a clinical laboratory. Thereare minimal methods currently available for at home sample collectionand nucleic acid extraction for diagnostic analysis. The devicesdisclosed herein provide an over the counter solution for nucleic acidextraction with or without nucleic acid amplification and with orwithout a reaction comprising a programmable nuclease, guide nucleicacid, and a reporter, such as the DETECTR reaction. The resultingproducts from any or all of these modules are applied to a readoutdevice for data collection and subsequent analysis.

A crude sample preparation protocol includes elution of a sample from asample collection device (e.g. swab) into a buffer that will inducedissociation of the sample into its macromolecule components releasingthe genomic nucleic acids. Buffer conditions used to induce thedissociation include any or all of the following: pH change, chaotropicsalts and a detergent (Tween 20, TRITON X-100, Deoxycholate, Sodiumlaurel sulfate or CHAPS. This protocol occurs in a stepwise work flowthat would feed into a hand held device. In this device there is atleast one chamber that contains the reagents components for the samplepreparation protocol.

FIG. 28 shows individual parts of sample preparation devices of thepresent disclosure. Part A of the figure shows a single chamber sampleextraction device: (a) the insert holds the sample collection device andregulates the step between sample extraction and dispensing the sampleinto another reaction or detection device, (b) the single chambercontains extraction buffer. Part B of the figure shows filling thedispensing chamber with material that further purifies the nucleic acidas it is dispensed is an option: (a) the insert holds the samplecollection device and regulates the “stages” of sample extraction andnucleic acid amplification. Each set of notches (red, blue and green)are offset 900 from the preceding set, (b) the reaction module containsmultiple chambers separated by substrates that allow for independentreactions to occur. (e.g., i. a nucleic acid separation chamber, ii. anucleic acid amplification chamber and iii. a DETECTR reaction chamberor dispensing chamber). Each chamber has notches (black) that preventthe insert from progressing into the next chamber without a deliberate900 turn. The first two chambers may be separated by material thatremoves inhibitors between the extraction and amplification reactions.Part C shows options for the reaction/dispensing chamber: (a) a singledispensing chamber may release only extracted sample orextraction/amplification or extraction/amplification/DETECTR reactions,(b) a duel dispensing chamber may release extraction/multiplexamplification products, and (c) a quadruple dispensing chamber wouldallow for multiplexing amplification and single DETECTR or four singleamplification reactions.

FIG. 29 shows a sample work flow using a sample processing device. Thesample collection device is attached to the insert portion of the sampleprocessing device (A). The insert is placed into the device chamber andpressed until the first stop (lower tabs on top portion meet upper tabson bottom portion) (B). This step allows the sample to come into contactwith the nucleic acid extraction reagents. After the appropriate amountof time, the insert is turned 900 (C) and depressed (D) to the next setof notches. These actions transfer the sample into the amplificationchamber. The sample collection device is no longer in contact with thesample or amplification products. After the appropriate incubation, theinsert is rotated 90 (E) and depressed (F) to the next set of notches.These actions release the sample into the DETECTR (green reaction). Theinsert is again turned 90° (G) and depressed (H) to dispense thereaction.

Examples of crude sample preparation protocols are summarized in TABLE11.

TABLE 11 Incubation Incubation Name Sample HCl Detergent Urea timetemperature Low pH Clinical Yes N/A No 15 minutes RT reminant Low pH +heat Clinical Yes N/A No 15 minutes 60° C. reminant DeoxycholateClinical No Yes No 15 minutes RT reminant Deoxycholate + Clinical No YesNo 15 minutes 60° C. heat reminant CHAPS Clinical No Yes No 15 minutesRT reminant CHAPS + heat Clinical No Yes No 15 minutes 60° C. reminantDeoxycholate + Clinical No Yes Yes 15 minutes RT Urea reminantDeoxycholate + Clinical No Yes Yes 15 minutes 60° C. Urea + heatreminant CHAPS + Clinical No Yes Yes 15 minutes RT Urea reminant CHAPS +Clinical No Yes Yes 15 minutes 60° C. Urea + heat reminant NucleoSpinClinical No Yes Yes  3 minutes RT Control reminant

FIG. 30 shows extraction buffers used to extract Influenza A RNA fromremnant clinical samples. Replicate remnant clinical samples wereexposed to the reagents listed in TABLE 11 above. The extraction processwas completed using the NucleoSpin Virus kit. qPCR analysis wasperformed to evaluate the quality and quantity of extracted RNA genome.The low pH condition resulted in RNA amounts equal to the sampleextracted with the ‘gold standard’ kit (RT-pool).

FIG. 31 shows that low pH conditions allow for rapid extraction ofInfluenza A genomic RNA. Decreasing time of exposure to low pHconditions did not affect the efficiency of viral dissociation andsubsequent extraction completed using the NucleoSpin Virus kit. Theamount of extracted product was similar to the ‘gold standard’extractions (RT-pool).

Example 34 Isothermal Amplification in CRISPR-Cas Diagnostics

This example describes methods of isothermal amplification in theprogrammable nuclease diagnostics of the present disclosure. Here,CRISPR-Cas diagnostics were used as programmable nuclease diagnostics ofthe present disclosure, including those diagnostics involving DETECTRassays. CRISPR diagnostics leverage the unique biochemical properties ofType V (e.g. Cas12) and Type VI (e.g. Cas13) CRISPR-Cas proteins toenable the specific detection of nucleic acids. These proteins aredirected to their target nucleic acid by a CRISPR RNA (crRNA), which isalso known as a guide RNA (gRNA). Once bound to a complementary targetsequence, the Cas protein initiates indiscriminate cleavage ofsurrounding single-strand DNA or single-strand RNA. When coupled to aquenched fluorescence reporter or other cleavage reporter, fluorescentor other signal can be generated by the Cas protein only in the presenceof the target nucleic acid. Alone these proteins are capable ofdetecting in the pM or fM range of target nucleic acid. When coupled tonucleic acid amplification set forth in this example and disclosedelsewhere herein, the sensitivity of CRISPR diagnostics was increased tothe aM or zM range. PCR is a commonly used nucleic acid amplificationmethod that generates double stranded DNA (dsDNA) when temperatures arecycled between two or three different temperatures. Nucleic acidamplification methods that function at single temperature are known asisothermal amplification. These methods include loop-mediated isothermalamplification (LAMP), recombinase polymerase amplification (RPA), strandinvasion based amplification (SIBA), strand displacement amplification(SDA), and nucleic acid sequence based amplification (NASBA). Thesemethods can be coupled to reverse transcription (RT) which enables thesemethods to amplify RNA targets by first converting the RNA to cDNAthrough reverse transcription.

CRISPR based diagnostics using Type V (e.g., Cas12) and CasVI (e.g.,Cas13) proteins were run using isothermal amplification methods oftarget nucleic acids to enable sensitive diagnostic assays.

RPA. Recombinase polymerase amplification (RPA) was used to amplify DNAsequences or RNA sequences by including a reverse transcription enzymein the reaction (RT-RPA). RPA and RT-RPA can be used to generate anamplicon suitable for detection by Type V (e.g. Cas12) Cas proteins.

FIG. 32 shows the application of RT-RPA to the detection of Influenza A,Influenza B, and human Respiratory Syncytial Virus (RSV) viral RNA byCas12a. A DNA or RNA sequence was amplified using RPA or RT-RPA prior todetection. By including a T7 promoter on one of the RPA primers, an invitro transcription (IVT) reaction using an RNA polymerase to convertRNA to DNA step was performed after the RPA reaction to generate targetRNA for detection by Type VI (e.g. Cas13) proteins. In FIG. 32 ,detection of RT-RPA amplicon was carried out from 4000 copies ofInfluenza A (IAV), Influenza B (IBV), and human respiratory syncytialvirus (RSV) RNA using Cas12a. The RT-RPA reaction was performed at 40°C. for 30 minutes. Controls included no RT enzyme, no target control,and no primer control. Following the RT-RPA reaction, the RT-RPAamplicon was transferred to a Cas12a DETECTR assay.

FIG. 33 shows the application of RT-RPA coupled with an IVT reactionenabling detection of viral RNA using Cas13a. In FIG. 33 , detection ofRT-RPA amplicon was carried out from 2 fM of PPR virus RNA using Cas13a.The RT-RPA reaction was performed at 40° C. for 30 minutes. Severalreverse transcriptase enzymes were evaluated for their compatibilitywith the RPA reaction. Controls included no RT enzymes, no target, andno primers. Following the RT-RPA reaction, the RT-RPA amplicon wastransferred to an IVT reaction for generation of RNA at 37° C. for 10minutes. The product of the IVT reaction was diluted and added to aCas13a reaction at 37° C. On-target and off-target crRNAs were used todemonstrate specificity of the Cas13a reaction.

A “two-pot” DETECTR assay was carried out using RPA and Cas13a bycombining the IVT reaction with the RT-RPA or RPA reaction to generateRNA simultaneously with the RPA reaction. FIG. 34 shows the productionof RNA, as detected by Cas13a, from an RNA virus using an RT-RPA-IVT“two-pot” reaction. In the two-pot reaction, the first reaction was theRT-RPA-IVT, and the second reaction as the Cas13a detection assay.Components of the IVT (T7 RNA polymerase, NTPs) were added to a RT-RPAreaction in the presence of RNA transcription buffer (RPA rehydrationbuffer from Twist Dx “buffer 1”) or RPA rehydration buffer (20 mMimidazole, pH 7.5; 50 mM KCl; 5 mM MgCl₂; BSA 10 pg/mL; 0.01% IgepalCa-630; 5% glycerol “buffer 2”). As a control, RT-RPA without the RNApolymerase was added. 2 fM of PPR virus RNA was used as the target RNAin these reactions. The reaction proceeded for 15 minutes at 37° C. andon-target and off-target crRNAs were used to show specificity.

The IVT and Cas13a detection assay reactions were combined with RT-RPAor an RPA reaction to generate and detect RNA simultaneously in a“one-pot” assay. FIG. 35 shows the effect of various buffers on theperformance of a one-pot Cas13a assay. Components for RT-RPA werecombined in a single reaction with both components for IVT (T7 RNApolymerase, NTPs) and Cas13a detection (Cas13a enzyme, crRNA,fluorescent cleavage reporter). The reaction was run in three buffers(buffer 1: RPA rehydration buffer, buffer 2: Cas13a buffer, and buffer3: Cas12a buffer (20 mM Tris-HCl, pH 8.0; 100 mM NaCl; 5 mM MgCl₂; 1 mMDTT; 5% glycerol; 50 μg/mL heparin)). Reactions without the RNApolymerase were used as controls. In addition, specificity was shown bycomparing a reaction with an on-target crRNA to a reaction with anoff-target crRNA. The reaction was allowed to proceed at 40° C. for 10minutes.

FIG. 36 shows the specific detection of viral RNA from the PPR virusthat infects goats using the one-pot Cas13a assay. 500 aM of viral RNAwas added to the reaction and the reaction was incubated at 40° C. As acontrol, an identical reaction without the T7 RNA polymerase(“PPRV-noIVT”; graph at right) was used to show the specific productionof RNA for Cas13a to detect. An on-target and off-target crRNA was usedto demonstrate assay specificity.

FIG. 37 shows the specific detection of Influenza B using the one-potCas13a assay run at 40° C. Reagents for RPA or RT-RPA, in vitrotranscription, and Cas13a detection were combined in a single reaction.40 fM of viral RNA was added to the reaction. As a control, an identicalreaction without reverse transcriptase (labeled “−RT”) was used to showthe specific production of RNA for Cas13a to detect. An on-target andoff-target crRNA was used to demonstrate assay specificity.

FIG. 38 shows the tolerance of the one-pot Cas13a assay for thedetection of RNA from the Influenza B virus in the presence and in theabsence of a universal viral transport medium called universal transportmedia (UTM Copan) at 40° C. Reagents for RPA or RT-RPA, in vitrotranscription, and Cas13a detection were combined in a single reaction.40 fM of viral RNA was added to the reaction. As a control, an identicalreaction without reverse transcriptase (−RT) was used to show thespecific production of RNA for Cas13a to detect. An on-target andoff-target crRNA was used to demonstrate assay specificity.

FIG. 39 shows the one-pot Cas13a detection assay at varioustemperatures. FIG. 39A shows a schematic of the workflow includingproviding DNA/RNA and the one-pot reaction including RPA/RT-RPA, invitro transcription, and Cas13a detection. Reagents for RPA or RT-RPA,in vitro transcription, and Cas13a detection were combined in a singlereaction. FIG. 39B shows a graph of Cas13a detection of Influenza A RNAat various temperatures. FIG. 39C shows a graph of Cas13a detection ofInfluenza B RNA at various temperatures. FIG. 39D shows a graph ofCas13a detection of human RSV (FIG. 39D) RNA at various temperatures.100,000 viral genomes were added to the reaction and compared toreactions containing 0 copies. Reactions were run at either 30° C.,32.5° C., 35° C., 37.5° C., or 40° C. The assay was determined to bemost robust between 35° C. and 37.5° C.

LAMP. Loop-mediated isothermal amplification (LAMP) was also used foramplifying a DNA sequences or RNA sequences in combination with areverse transcriptase enzyme (RT-LAMP). LAMP reactions use a combinationof four, five, or six primers to amplify the target DNA or cDNA fromRNA. During the course of the LAMP reaction, concatemers of ampliconsform. If RT-LAMP or LAMP amplicons contain sequence features thatsupport Cas protein recognition (such as PAM or PFS), they can be usedas target nucleic acids in CRISPR diagnostics.

FIG. 40 shows the optimization of a LAMP reaction for the detection ofan internal amplification control using a DNA sequence derived from theMammuthus primigenius (Wooly Mammoth) mitochondria. In addition, FIG. 40shows the specific detection of the LAMP amplicon by Cas12a using avariety of crRNAs. FIG. 40A shows a schematic of the workflow includingproviding DNA/RNA, LAMP/RT-LAMP amplification, and Cas12a detection.FIG. 40B shows the time to result for LAMP reactions for an internalamplification control using a DNA sequence derived from the Mammuthusprimigenius, as quantified by fluorescence. The time to result wasdetermined by the time to reach half of max fluorescence for a reaction.Controls include off-target Hela genomic DNA and a no target control.FIG. 40C shows Cas12a specific detection at 37° C. of LAMP amplicon fromthe 68° C. temperature reaction. Two on-target crRNAs were tested.Specificity was shown by no detection from Hela genomic DNA amplicon orno template control (NTC) amplicon.

FIG. 41 shows the optimization of LAMP and Cas12 specific detection ofthe human POP7 gene that is a component of RNase P. This sequence ispresent in human DNA and RNA and was used as a control for theefficiency of sample extraction (sample control). FIG. 41A shows aschematic of the workflow including providing DNA/RNA, LAMP/RT-LAMPamplification, and Cas12a detection. FIG. 41B shows the time to resultof a LAMP/RT-LAMP reaction for RNase P POP7 at different temperatures,as quantified by fluorescence. Time to result was determined by the timeto reach half of max fluorescence for a reaction. Controls includedoff-target mouse-liver-RNA and a no target control. Hela total RNA andHela genomic RNA were detected by the RT-LAMP and LAMP reactions,respectively. FIG. 41C shows three graphs demonstrating Cas12a specificdetection at 37° C. of LAMP/RT-LAMP amplicon from the 68° C. temperaturereaction. Two on-target crRNAs were tested and one off-target crRNA wastested. Specificity was shown by no detection of mouse total RNAamplicon or no template control (NTC) amplicon.

Cas12 was also used for the detection of RT-LAMP products. FIG. 42 showsthe specific detection of three different RT-LAMP amplicons forInfluenza A virus. The data from this experiment shows that the designof RT-LAMP primers around Cas12a compatible sites was important for thespecificity of the experiment. The primer and crRNA were optimized andcombined for specific detection of Influenza A (IAV) amplified byRT-LAMP. Briefly, three different primer sets were tested for use inRT-LAMP reactions that were specific to IAV. RT-LAMP reactions wereperformed either in the presence of IAV RNA or as a control with notemplate (NTC). For each amplicon, two on-target crRNAs and oneoff-target crRNA was used in a Cas12a detection assay at 37° C.

FIG. 43 shows the identification of optimal crRNAs for the specificdetection of Influenza B (IBV) RT-LAMP amplicons. The RT-LAMP reactionwas performed for 30 minutes at 60° C. in the presence of Influenza A(IAV) RNA, IBV RNA, or a no template control (NTC). For the resultingamplicons, three on-target crRNAs were used to determine which was mostspecific and efficient for the detection of Influenza B by Cas12a at 37°C.

The primers of an RT-LAMP or LAMP reaction were combined for multiplexedamplification. Because of the formation of concatemers during RT-LAMPand LAMP, it is difficult to differentiate between amplicons in amultiplex RT-LAMP or LAMP reaction by conventional means (e.g., by gelelectrophoresis), as shown in FIG. 44 . Multiplexed RT-LAMP forInfluenza A (IAV) and Influenza B (IBV) was carried out for 30 minutesat 60° C. RT-LAMP reactions were incubated with 10,000 viral genomecopies of IAV, IBV, or both IAV and IBV. A no-target control (NTC) wasused that contained 0 viral genome copies. 0.5 μL of the RT-LAMP productafter the 30 minute incubation was run on a 1% agarose gel. FIG. 44shows the results of the 1% agarose gel with bands showing the productsof the RT-LAMP reaction. As seen in the gel, it is difficult todifferentiate between the IAV, IBV, and IAV+IBV samples. The applicationof Type V (e.g. Cas12) enzymes identified which amplicons were amplifiedin a multiplexed RT-LAMP or LAMP reaction. FIG. 45 shows Cas12adiscrimination between amplicons from a multiplex RT-LAMP reaction forInfluenza A and Influenza B. FIG. 45A shows a schematic of the workflowincluding providing viral RNA, multiplexed RT-LAMP amplification, andCas12a influenza A detection or Cas12a influenza B detection. FIG. 45Bshows Cas12a detection of RT-LAMP amplicons after 30 minute multiplexedRT-LAMP amplification at 60° C. Multiplexed amplification containedprimer sets for Influenza A (IAV) and Influenza B (IBV). Reactionscontained 10000 viral genome copies or 0 copies as a control. Targetsfor IAV only, IBV only, and IAV and IBV combined were used. FIG. 45Cshows background subtracted fluorescence at 30 minutes of Cas12adetection at 37° C. of RT-LAMP amplicons for 10,000 viral genome copiesof IAV and IBV. crRNAs specific for IAV and IBV enable discriminationfor which viral sample was present. Similarly, FIG. 46 shows Cas12adiscrimination between a triple multiplexed RT-LAMP reaction forInfluenza A, Influenza B, and the Mammuthus primigenius (Wooly Mammoth)mitochondria internal amplification control sequence after 30 minutes ofmultiplexed RT-LAMP amplification at 60° C. Multiplexed amplificationcontained primer sets for Influenza A (IAV), Influenza B (IBV), and theMammoth internal amplification control (Mammoth IAC). Reactionscontained 100,000 viral genome copies or 500 aM of the IAC. Targets forIAV only, IBV only, multiplexed IAV+IBV, and multiplexed IAV+IBV+MammothIAC were used. Cas12a detection assays at 37° C. with IAV, IBV, andMammoth IAC specific crRNAs were performed to differentiate theamplicons from the multiplexed reactions.

By including a T7 promoter sequence in the forward inner primers (FIP)or backward inner primers (BIP) of a LAMP or RT-LAMP reaction, theresulting amplicon can be added to an in vitro transcription reaction togenerate RNA, as shown in the schematic in FIG. 47 . This RNA can beused in a Type VI (e.g. Cas13) detection assay. FIG. 47A shows aschematic illustrating the identity of the primers used in LAMP andRT-LAMP. Primers LF and LB are option in some LAMP and RT-LAMP designs,but generally increase the efficiency of the reaction. FIG. 47B shows aschematic illustrating the position and orientation of the T7 promoterin a variety of LAMP primers.

FIG. 48 shows that a T7 promoter can be included on the F3 or B3 primers(outer primers), or FIP or BIP primers for Influenza A. However, only T7promoters located in the FIP or BIP primers are capable of generatingenough RNA to enable a Cas13a detection assay. FIG. 48A shows aschematic of the workflow including providing DNA/RNA, LAMP/RT-LAMPamplification, in vitro transcription, and Cas13a detection. FIG. 48Bshows the time to result for RT-LAMP reactions for Influenza A usingdifferent primer sets, as quantified by fluorescence. Each primer setcontained a T7 promoter sequence in a different position. Time to resultwas determined by the time to reach half of max fluorescence for areaction. No target was used as a specificity control. The resultsdemonstrated that the B3+T7 and BIP+T7 sense primer sets worked best forRT-LAMP reaction. The reaction was performed at 68° C. for 30 minutes.FIG. 48C shows in vitro transcription (IVT) with T7 RNA polymerase ofthe product of the RT-LAMP reactions for Influenza A using differentprimer sets at 37° C. for 10 minutes. A Cas13a detection assay at 37° C.was then used to detect the RNA products from the IVT reaction. Threedifferent on-target crRNAs were used along with an off-target crRNA todemonstrate specificity. The BIP+T7 sense and antisense primer setsworked best for RNA production, along with on-target crRNA #2. Thus, theBIP+T7 sense primer set in conjunction with crRNA #2 worked best for thedetection of RNA after a RT-LAMP reaction followed by an IVT reaction.

SIBA. Strand invasion based amplification (SIBA) is another isothermalmethod that can be used. FIG. 49 shows the detection of a RT-SIBAamplicon for Influenza A by Cas12. In SIBA and RT-SIBA reactions forCas12, the guide RNA is not complementary to the invasion oligo and theamplicon contains a PAM. The RT-SIBA reaction was performed at 41° C.for 60 minutes with a starting RNA concentration of 500 aM. Controls forthe RT-SIBA reaction included a no target control and a no primercontrol. After the completion of the RT-SIBA reaction, 2 μL of ampliconwas added to a 20 μL Cas12a detection reaction. On-target and off-targetcrRNAs were used to show specific detection of by Cas12.

Example 35 Optimization of Assay Conditions for ProgrammableNuclease-Based Diagnostic Assays

This example describes optimization of assay conditions for programmablenuclease diagnostic assays as disclosed herein. Here, the CRISPR-CasDETECTR-based diagnostic assays disclosed herein were used as theprogrammable nuclease diagnostic assays. The components of the DETECTRreaction, such as protein concentration, crRNA, and buffer componentsimpact the rate and efficiency of the reaction. Optimization of thebuffers allows for the development of an assay with increasedsensitivity and specificity.

Improvements to buffers and assay conditions were identified forCas13M26 (Lbu-Cas13a) included 100 ng/μL of tRNA. The performance of theoriginal buffer for Cas13a detection (including the 100 ng/μl of tRNA)is shown on the graph is the middle-most line. Cas13a was incubated with1 pM of target RNA at 37° C. with varying concentrations of tRNA in thereaction buffer. As a control, the assay was also performed with 0 pM ofthe target RNA. FIG. 50 shows graphs of activity, as measured byfluorescence, with (left graph) and without (right graph) activator overtime. FIG. 50 shows that increasing the amount of tRNA in the reactiondecreases the efficiency of the Cas13a detection assay. Similarly,decreasing the amount of tRNA in the reaction or eliminating itcompletely, increases the efficiency of the Cas13a detection assaywithout dramatically changing the stability of the reaction in theabsence of activator.

Urea is an additive that is used to increase the efficiency of someenzymatic reactions, such as proteinase K digestion, and is present inurine. To evaluate inhibition of Cas13a activity in the DETECTR assays,1 pM of target RNA at 37° C. was incubated with varying concentrationsof urea. The activator, shown in the following graphs, is the targetRNA. FIG. 51 shows inhibition of Cas13a activity by SDS and urea. FIG.51A shows the Cas13a detection assay performed in the presence of 0-200mM urea. Concentrations above 300 mM urea inhibited the assay (leftgraph shows with activator and right graph shows without activator). Theorange line indicates the performance of the assay with 0 mM urea (acontrol showing uninhibited Cas13a activity). SDS is a common inhibitorof RNases and is used to eliminate RNase contamination and denatureproteins. To evaluate inhibition of Cas13a activity in DETECTR assays, 1pM target RNA at 37C was incubated with varying amounts of SDS. FIG. 51Bshows complete inhibition of Cas13a upon addition of 0.1% or greateramounts of SDS to the reaction (left graph shows with activator andright graph shows without activator). The orange line indicatesperformance of Cas13a with 0% SDS (a control showing uninhibited Cas13aactivity).

The importance of salt type and salt concentration on the performance ofCas13a in a DETECTR assay was evaluated. DETECTR assays were performedwith 10 pM of target or 0 pM of target (control). FIG. 52 shows theperformance of Cas13a in DETECTR reactions with varying concentrationsof salt. FIG. 52A shows the results of varying the concentration of NaClin a Cas13a DETECTR reaction. FIG. 52B shows the results of varying theconcentration of KCl in a Cas13a DETECTR reaction. Cas13a performedcomparably between NaCl and KCl salt types. Cas13a performance decreasedat 30 mM salt and below, and was inhibited by salt concentrations above80 mM.

The importance of DTT in different salt types and its impact on Cas13aperformance in a DETECTR assay was evaluated. DTT is used to stabilizeproteins, such as RNase inhibitors, and increase the efficiency of someenzymes. DETECTR assays were carried out using Cas13a for detection of10 pM of target or no target (control). FIG. 53 shows optimization ofDTT concentration in a Cas13a DETECTR assay. FIG. 53A shows varying DTTconcentration in NaCl. FIG. 53B shows varying DTT concentrations in KCl.The orange bar indicates original buffer conditions (50 mM KCl) and noDTT. The results showed that the Cas13a DETECTR assay was not affectedby DTT concentrations from 0-10 mM in buffers containing either NaCl orKCl.

Reporter choice for the Cas13a DETECTR assay was evaluated. The quenchedfluorescent reporter generates the fluorescent signal that is used tomonitor Cas13a detection performance in the DETECTR assays. A variety ofdifferent RNA reporter sequences was evaluated for their impact on assayperformance. Cas13a detection assays were performed with either 1 pMtarget RNA or no target RNA at 37° C. Reactions were performed in eitherthe standard Cas13a reaction buffer (HEPES pH 6.8 buffer with tRNA; 20mM HEPES, pH 6.8; 50 mM KCl; 5 mM MgCl₂; 10 μg/mL BSA; 100 μg/mL tRNA;0.01% Igepal Ca-630; 5% glycerol) or in an identical buffer that lackedbackground tRNA “RNAlessPB”. FIG. 54 shows the activity of Cas13a in theDETECTR assay, as measured by fluorescence, for each of the testedreporters. The “U5” reporter (/5-6FAM/rUrUrUrUrU(SEQ ID NO: 1)/3IABkFQ/)and the “UU” reporter (/56-FAM/TArUrUGC/3IABkFQ/) exhibited the bestperformance. A reporter with the same nucleotide sequence as the “U5”reporter but with a different fluorophore and quencher, “TYE665U5”(/5-TYE665/rUrUrUrUrU(SEQ ID NO: 1)/3IABkRQ/) also performed well.Increasing the length of the reporter generated higher background inprocessing buffers that did not contain background RNA.

The optimal buffer composition and pH for Cas13a DETECTR assays wasidentified. To determine the ideal buffer and pH for the Cas13adetection assay, 84 different combinations of buffers and pH weretested. The final buffer concentration used in each assay was 20 mM.Aside from the buffer itself, the remaining assay components included 50mM KCl, 5 mM MgCl₂, 10 μg/mL BSA, 100 μg/ML tRNA, 0.01% Igepal Ca-630,and 5% Glycerol. Cas13a DETECTR assays were performed with 1 pM targetRNA or no target RNA as a control. The dotted line indicates performanceof the standard Cas13a reaction buffer (also referred to as “HEPES pH6.8 buffer”; HEPES pH 6.8 buffer with tRNA; 20 mM HEPES, pH 6.8; 50 mMKCl; 5 mM MgCl₂; 10 μg/mL BSA; 100 μg/mL tRNA; 0.01% Igepal Ca-630; 5%glycerol). Dots indicate replicates. FIG. 55 shows Cas13a activity inthe DETECTR assay, as measured by fluorescence, for each of the testedconditions. These results demonstrated that the optimal pH is around 7.5and that the imidazole, phosphate, tricine, and SPG buffers are all highperforming buffers, in comparison to the original HEPES pH 6.8 buffer.Cas13a detection was inhibited at pH values below 6.5. Dots indicatereplicates, while bar height indicates the mean of the replicates.

Cas13a activity in DETECTR assays was assessed in a variety ofcommercially available buffers. Cas13a detection assays were carried outwith either 1 pM target RNA or no target RNA at 37° C. Reactions wereperformed either in the presence or absence of 100 ng/μL tRNA. Buffersused included NEB1 (NEBuffer1, New England Biolabs (NEB)), NEB2(NEBuffer2, NEB), NEB3 (NEBuffer3, NEB), Cutsmart (NEB), RNPB (RNApolymerase buffer, NEB), and the HEPES pH 6.8 buffer. These buffercompositions are as follows: NEBuffer 1.1 (1× Buffer Components, 10 mMBis-Tris-Propane-HCl, 10 mM MgCl₂, 100 g/ml BSA, pH 7.0 at 25° C.);NEBuffer 2.1 (1× Buffer Components, 50 mM NaCl, 10 mM Tris-HCl, 10 mMMgCl₂, 100 g/ml BSA, pH 7.9 at 25° C.); NEBuffer 3.1 (1× BufferComponents, 100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl₂, 100 g/ml BSA, pH7.9 at 25° C.); CutSmart Buffer (1× Buffer Components, 50 mM PotassiumAcetate, 20 mM Tris-acetate, 10 mM Magnesium Acetate, 100 g/ml BSA, pH7.9 at 25° C.); and 1× RNAPol Reaction Buffer (40 mM Tris-HCl, 6 mMMgCl₂, 1 mM DTT, 2 mM spermidine (pH 7.9 at 25° C.)). The resultsdemonstrated that Cas13a performance improved in NEBuffer2 and Cutsmartin comparison to the HEPES pH 6.8 buffer. FIG. 56 shows Cas13aperformance in the DETECTR assay, as measured by fluorescence, for eachof the five commercially available buffers and the original HEPES pH 6.8buffer.

Combining the above described observations of buffer performance, anoptimized Cas13a buffer called MBuffer1 was developed. 1× MBuffer1includes 20 mM imidazole pH 7.5, 50 mM KCl, 5 mM MgCl₂, 10 μg/pL BSA,0.01% Igepal Ca-630, and 5% glycerol. FIG. 57 shows a head-to-headcomparison of the HEPES pH 6.8 buffer to the optimized MBuffer1 for aCas13a DETECTR assay with serially diluted target RNAs and run at 37° C.for 30 minutes. The limit of detection for the HEPES pH 6.8 buffer wasaround 1 pM, whereas the limit of detection for MBuffer1 was found to bebetween 100 fM and 10 fM. Thus, FIG. 57 demonstrates that there is a 10×and 100× improvement in assay performance using MBuffer1.

Cas13a performance in DETECTR assays was evaluated with and withoutglycerol. Glycerol is commonly used in many enzymatic buffers. Cas13adetection assays with varying concentrations of target RNA were run at37° C. for 30 minutes in either MBuffer1 with glycerol or MBuffer1without glycerol. FIG. 58 shows that 5% glycerol in MBuffer1 (leftgraph) increases assay performance in comparison to an identical bufferwithout glycerol (right graph).

Cas13a performance in DETECTR assays was evaluated with varyingconcentrations of BSA and NP-40. BSA and NP-40 (Igeca1-Ca 630) are usedin many enzymatic buffers to increase assay performance and decreasebinding of the protein to plastic surfaces. Cas13a DETECTR assays wererun with 1 pM target RNA or no target RNA at 37° C. for 30 minutes inMBuffer1 with varying concentrations and combinations of NP-40 (IgepalCa-630) and BSA. FIG. 59 shows a gradient chart of Cas13a activity inthe DETECTR assay, as measured by fluorescence, (darker squares indicateincreased Cas13a activity) versus varying NP-40 concentration along thex-axis and varying BSA concentration along the y-axis. The resultsindicated that both BSA and NP-40 improve the assay. NP-40 (Igeca1-Ca630) was found to be important for the efficiency of the Cas13adetection assay. Small amounts of BSA also improved the performance ofthe assay. Concentrations of 0.05% to 0.0625% NP-40 were most optimaland concentrations of 2.5 to 0.625 μg/mL BSA were most optimal. BSA didnot improve assay performance unless NP-40 was also present.

To determine which types of compounds may increase or inhibit theperformance of Cas13a in DETECTR assays, assays were run with 96different additives (JBScreen Plus HTS, Jena Biosciences). Additivesfrom the Jena Biosciences plate were diluted 1:66 into the final Cas13aDETECTR assay with 100 pM of target. FIG. 60 shows Cas13a performance inDETECTR assays, as measured by fluorescence, versus the differentadditives tested. Results showed that the specific compounds thatinhibited the performance of the assay included: beryllium sulfate,manganese chloride, zinc chloride, tri-sodium citrate, copper chloride,yttrium chloride, 1-6-Diaminohexane, 1-8-diaminooctane, ammoniumfluoride, ethanolamine, lithium salicylate, magnesium sulfate, potassiumcyanate, and sodium fluoride.

The original buffer developed for Lba-Cas12a used Tris pH 7.5. FIG. 61shows the results of screening 84 different buffer and pH combinationsto determine the optimal buffer for Lba-Cas12a activity in DETECTRassays, as measured by fluorescence. A final buffer concentration of 20mM was used for each assay. The remaining assay components included 100mM KCl, 5 mM MgCl₂, 50 μg/mL heparin, 1 mM DTT, and 5% Glycerol.Lba-Cas12a DETECTR assays were performed at 37° C. with 100 pM targetDNA or no target DNA as a control. The dotted line indicates performanceof the original buffer. Dots indicate replicates, while the bar heightindicates the mean of the replicates. Results of this experiment showedthat Lba-Cas12a prefers pH 8.0 and works well in AMPD, BIS-TRISpropane,DIPSO, HEPES, MOPS, TAPS, TRIS, and tricine buffers. Lba-Cas12a wasinhibited at pH 6.5 and below and was not functional in phosphate,succinate, malonate, citrate, MES, and ADA buffers.

The optimal salt type and salt concentration was determined forLba-Cas12a performance in DETECTR assays. Lba-Cas12a DETECTR assays wererun with 10 pM of target DNA or no target DNA at 37° C. for 30 minuteswith varying concentrations of KCl. FIG. 62 shows Lba-Cas12a performancein DETECTR assays, as measured by fluorescence, in each of the testedconditions. Results indicated that the Lba-Cas12a performed best inassays with low KCl concentrations (0-40 mM or less than 20 mM salt andless KCl). Above 80 mM the assay was inhibited, with little to noactivity above 160 mM.

The optimal buffer type and pH was determined for the Type V CRISPR-Casprotein Cas12M08 performance in DETECTR assays. FIG. 63 shows Cas12M08performance in DETECTR assays, as measured by fluorescence, for each ofthe tested conditions (buffer type and pH). The final concentration ofbuffer in each assay was 20 mM. The remaining assay components included120 mM NaCl, 5 mM MgCl₂, and 1% Glycerol. Cas12M08 DETECTR assays wereperformed at 37° C. with 1 nM target DNA or no target DNA as a control.The dotted line indicates the performance of the buffer used in Cas12M08DETECTR assays (20 mM Tris-HCl, pH 7.5; 120 mM NaCl; 5 mM MgCl₂; 1%glycerol). Results showed that Cas12M08 performed optimally in a pH of7.5. High performance buffers included DIPSO, HEPES, MOPS, TAPS,imidazole, and tricine. Cas12M08 was inhibited in Tris buffers, but wasstill functional. Cas12M08 showed little or no functional activity insuccincate, malonate, MES, ADA, citrate, SPG, and phosphate buffers.

Further investigation of the optimal buffer type and pH was carried outfor Cas12M08. Some proteins prefer buffers that have reduced numbers ofchloride ions. To determine whether Cas12M08 performed better inchloride—(“C1”) or acetate-based (“Acetate”) buffers, a screen of salttype and concentration was carried out. FIG. 64 shows Cas12M08performance in DETECTR assays, as measured by fluorescence, for thevarious salt types and concentrations tested. Assay components included20 mM HEPES pH 7.3, 1% Glycerol, and 5 mM of MgCl or MgOAc. Varyingamounts of KCl or KOAc were screened with the corresponding magnesiumtype. Cas12M08 detection assays ere carried out at 37° C. with 1 nMtarget DNA and no target DNA as a control for 30 minutes. Cas12M08performed best at a salt concentration of around 4 mM (ranging from 2-10nM) and showed increased activity in buffers with MgOAc and KOAc(acetate-based buffers, “Acetate”), in comparison to buffers with MgCland KCl (chloride-based buffers, “C1”).

The optimal concentrations of heparin and salt concentrations weredetermined for Cas12M08, since a relationship was observed between saltand heparin for SNP sensitivity using Lba-Cas12a. The base bufferincluded 20 mM HEPES pH 7.3, 5 mM MgOAc, and 1% Glycerol. Varyingamounts of KOAc and heparin were screened. Cas12M08 DETECTR assays wereperformed at 37° C. with 1 nM target DNA or no target DNA as a controlfor 30 minutes. For Lba-Cas12a heparin and salt concentrations combinedto affect the specificity of the enzyme. FIG. 65 shows Cas12M08performance in DETECTR assays, as measured by fluorescence (darkersquares indicate greater fluorescence and more activity), versus heparinconcentration on the x-axis and KOAc buffer concentration on the y-axis.The results of this experiment indicated that Cas12M08 was inhibited byheparin and prefers low salt.

Inhibitors and enhancers of assay performance were evaluated forCas12M08 DETECTR assays. DETECTR assays were run with 96 differentadditives (JBScreen Plus HTS, Jena Biosciences). Additives from the JenaBiosciences plate were diluted 1:66 into a final Cas12M08 detectionsassay with 1 nM of target. FIG. 66 shows that specific compoundsinhibited the performance of the assay including: benzamidinehydrochloride, beryllium sulfate, manganese chloride, potassium bromide,sodium iodine, zinc chloride, di-ammonium hydrogen phosphate,tri-lithium citrate, tri-sodium citrate, cadmium chloride, copperchloride, yttrium chloride, 1-6 diaminohexane, 1-8-diaminooctane,ammonium fluoride, and ammonium sulfate. Compounds that increased assayperformance included: polyvinyl alcohol type II, DTT, DMSO,polyvinylpyrrolidone K15, polyethylene glycol (PEG) 600, andpolypropylene glycol 400.

The positions along a target sequence most sensitive to single mutationswas identified by tiling all nucleotide possibility (A, T, C, G) at the20 positions downstream of the PAM motif along a Cas12M08 target site onHERC2 and ALDH. FIG. 67 shows the results of evaluating SNP sensitivityalong target sequences for Cas12M08. Squares with a bolded outlineindicate the WT sequence that matched the crRNA was used to interrogatethe sensitivity of Cas12M08 to mutations along a target site on HERC2and ALDH. Results indicated stronger SNP differentiation for Cas12M08along the 3′ end of the crRNA (distal from the PAM). A similarcomplementary experiment using Lba-Cas12a using the same sets of targetsites and crRNAs was carried out. FIG. 68 shows the results ofevaluating SNP sensitivity along target sequences for Lba-Cas12a.Lba-Cas12a displayed strong mutation sensitivity at all positions alongHERC2, and sensitivity on the PAM proximal (complementary to the 5′ endof the crRNA target sequence) on ALDH2. This suggested that Lba-Cas12awas more sensitive to mutations in this region and that mutationsensitivity as target site dependent.

Example 36 Lateral Flow Test Strips for Visual Detection of TargetNucleic Acids Using a Programmable Nuclease System

This example describes a lateral flow test-strip for visual detection ofreactions using a programmable nuclease system. Here, the DETECTRreactions using CRISPR-Cas systems were used as the reactions using theprogrammable nuclease systems.

Visual readouts for the DETECTR reaction were developed to have alow-cost format and be amenable to high-volume manufacturing. Describedhere are custom-made lateral flow strips. Colloidal gold nanoparticleswere conjugated to antibodies and the gold nanoparticles served as thevisual readout in the assay. Two commercially available lateral flowstrips were also tested including: (1) Millenia Hybridetect 1, TwistDx(UK, now part of Abbott) and (2) PCRD, Abingdon Health (UK).

Results were collected by: (1) visual inspection of the strips, and (2)obtaining a cell-phone-camera picture of the strips.

Unlike commercially available lateral flow test strips, the custom-madelateral flow strip design disclosed herein includes a new type ofCRISPR-Cas reporter molecule, which is made of (1) a 6-Fluorescein (FAM)moiety; (2) a biotin moiety; and (3) a DNA-based oligo linker, whichwill be irreversibly conjugated to the DETECTR reaction chamber upstreamof the reaction.

Lateral Flow Strips for Read Out of Cas12M08 and Lba-Cas12a. Lateralflow strips were tested for readout of Cas12M08 and Lba-Cas12a.Complexing reactions included final concentrations of 40 nM of crRNA perreaction, 40 nM of final protein per reaction, and 500 nM of reporterper reaction. Complexing reactions were incubated at 37C for 30 min, thereporter substrate was added, and 15 μl of the complexing reactions werealiquoted into PCR tubes. 5 μl of diluted PPR virus PCR product wasadded and the target and complex were incubated at 37C for 20 min. 100μl of MIlenia GenLine Dipstick Assay Buffer (Tween or TRITON) was addedand the dipstick was inserted into the solution with target and complex.Test strips were photographed and the top band was quantified usingImageJ.

FIG. 69A shows a photograph of test strips, which from left to rightshow Lba-Cas12a with target, Lba-Cas12a without target, Cas12M08 withtarget, and Cas12M08 without target.

FIG. 69B shows a graph of absorbance on the y-axis for each group tested(Lba-Cas12a with target, Lba-Cas12a without target, Cas12M08 withtarget, and Cas12M08 without target). The y-axis shows absorbance asquantified by ImageJ.

MNT-Lateral Flow, Au NP Conjugation. Anti-FAM and anti-ROX polyclonalantibodies were conjugated to gold nanoparticles for downstream use inthe custom made lateral flow strips. Materials include Corning Spin-×UF500 μl Concentrators and a Gold in a Box Conjugation kit. A 0.5× buffersolution was prepared by diluting PBS, pH 7.2 (1×) in 1:1 withnuclease-free water. 100 μl of the MNT antibody and 100 μl of a FITCantibody were used. Spin concentrators were used to exchange nativebuffer from 0.1M Tris glycerine, pH 7 with 10% glycerol to 0.5×PBS forboth antibodies. Washes with 100 μl of 0.5×PBS was carried out and theconcentrators were spun for 1.5 min at 18,000 rcg (xg) for each wash.Antibodies were eluted in 100 μl of 0.5×PBS. Gold conjugation wascarried out as per manufacturer's instructions. Tubes were labeledMNT1-10 and FITC1-10 and 7 μl of each antibody was added. Reactions wereincubated for 30 min in a shaking incubator at room temperature. Thereaction was stopped by adding 50 μl of a BSA blocking buffer to eachtubes, and tubes were stored at 4C.

Lateral Flow Strips for Read Out of Cas13M. Lateral flow strips weretested for readout of Cas13M. TwistDx lateral flow strips were used totest the FAM-U5-Biotin (rep71 reporter). Assays were run at roomtemperature at a variety of target concentrations. Complexing reactionsincluded final concentrations of 40 nM of crRNA per reaction, 40 nM offinal protein per reaction, and 500 nM of reporter per reaction.Complexing reactions were incubated at 37C for 30 min. Dilutions of thetarget were added to the reaction including at 10 nM, 1 nM, 0.1 nM, 0.01nM, and no target. 30 μl of the complexing reaction was added to thetarget and incubated for 15 minutes at room temperature. The reactionwas placed on ice and 10 μl of the reaction was pipetted directly ontothe lateral flow sample area. 50 μl of Milenia GenLine Dipstick Assaybuffer was added and the strip was photographed.

FIG. 69C shows a photograph of various test strips from Cas13M DETECTRassays with, from left to right, 10 nM, 1 nM, 0.1 nM, 0.01 nM, targetDNA, no target DNA, or water only.

Conjugation of 3′Amino Reporter to NHS Beads Using Kit. An NHS FlexiBindMagnetic Bead Kit was used to conjugate the 3′ amino modified lateralflow reporter that allowed for the intended usage of the lateral flowdevices (Milenia Hybrid), where the ligand is detected first and thecontrol line serves as the flow control. The sequence of the reporterused was/56-FAM/*/iBiodT/*AATTAATTAATTAATTAATT/3AmMO/(SEQ ID NO: 170).

Bead Conjugation was carried out as follows. Rep75 was resuspended to100 pM in Wash/Coupling Buffer (PBS, pH 7.4). 32.5 nmol was deliveredfrom IDT and 5.4 nmol (54 μL) of rep75 was used. Resuspend of the 20%NHS FlexiBind Magnetic beads was resuspended by vortexing for 20seconds. 100 μL of bead slurry was pipetted into a 1.5 mLmicrocentrifuge tube. Magnetic beads were pelleted on the magnetic standuntil the solution became clear. Storage buffer was removed anddiscarded. 100 μL of ice-cold Equilibration buffer (1 mM HCl) wasimmediately added. The reaction was removed from the magnet and vortexedfor 20 seconds then placed back on the magnet to pellet beads. Thesupernatant was removed and discarded and 54 μL of 100 pM rep75 in PBSwas added. Beads were incubated at room temperature with intervalmixing: 2 min rest, 15 sec mix at 1200 rpm for 2 hours. Tubes wereplaced in a magnetic stand to allow the beads to migrate to the magnet.Unbound ligand was removed and saved for analysis.

0.5 μL raw reporter was measured in 20 μL NFW vs. 0.5 μLpost-conjugation supernatant in 20 μL NFW on a plate reader until it wasno longer visibly green. 500 μL of Quench buffer was added, vortexed for30 seconds, and pelleted with a magnetic rack. The supernatant wasdiscarded and the sample was washed 5 times. Beads were resuspended in500 μL of Quench Buffer and incubated for 1 hour at room temperature.The beads were pelleted with a magnetic rack and the buffer was removedand discarded. The beads were resuspended in 100 μL of Wash/CouplingBuffer (PBS, pH 7.4) and the beads were kept on ice in dark tube.

Testing uncleaved/unconjugated reporter with lateral flow was carriedout using 2×NG-40-B009 Naked Gold Sol beads-40 nm-15 OD-9 mL, FITCantibody (Invitrogen TB265150), anti-IgG (Invitrogen A16098),Streptavadin (NEB N7021S), pH 8.8, and three batches—Batch 1: AU (5μL)→anti-IgG (1 μL)→Strep (0.5 μL), Batch 2: AU (5 μL)→strep (1μL)→anti-IgG (1 μL), and Batch 3: AU (2.5 μL)→strep (1 μL)→anti-IgG (1μL).

Test beads with Cas12M08 by first complexing reaction. Reactions wererun with final concentrations of 40 nM crRNA per reaction, 40 nM proteinper reaction, and 100, 250, 500, or 1000 nM reporter per reaction. Thecomplex was incubated at 37° C. for 30 min. The 40 pM stock of beads wasdiluted to 1:10 to 4 pM. Reporter beads were added to 5 μL PPRV dilutedPCR product or NFW, 15 μL of complexing reaction was added to target.The reaction was incubated at 37C for 30 min with shaking at 2000 rpm inThermomixer. Beads were pelleted with magnetic rack for 2 minutes. 10 μLof reaction was transferred to a new tube, 50 μL of Dipstick AssayBuffer was added, and 60 μL diluted reaction was placed on magnet beforeadding solution to lateral flow strips. Reactions were run on Mileniaflow strips.

FIG. 70 shows the layout of a Milenia commercial strip with a typicalreporter. This schematic shows an analyte-independent universal dipstickwith a sample application region at right followed by a wicking regionimmediately to the left, followed to the left by a region containing abiotin ligand, followed to the left by a region spotted with anti-rabbitantibody. The sample and analyte-specific solution are incubated withanalyte detectors bearing a biotin or FITC. Samples are run on thestrip. A positive result shows two bands—the left-most band is from thecontrol band and is due to binding of anti-FITC antibody coated goldnanoparticles to an anti-rabbit antibody. The right band is from thetest band itself and is due to binding by the biotin ligand to ananalyte detector bearing biotin, where the detector complexes theanalyte and wherein the analyte is further complexed to another detectorbearing FITC, which is then bound to the anti-FITC antibody coated goldparticle. In the negative result—only one band is seen at the controlline.

FIG. 71 shows the layout of a Milenia HybridDetect 1 strip with anamplicon. This schematic shows at top PCR amplicon using FAM and biotinprimers at the right end of the top figure. In the case of a positiveresult, the strip shows two bands—this PCR amplicon binds to a moietyimmobilized at the test line, and the FAM molecule (shown as a start)binds to an anti-FAM antibody coated particle. To the left of the testline is a flow control line, containing anti-rabbit antibody which bindsto anti-FAM antibody coated nanoparticles. In the case of a negativeresult, the strip shows one band—that is, just binding of anti-FAMantibody coated nanoparticles bound to anti-rabbit antibody immobilizedon the test strip.

FIG. 72 shows the layout of a Milenia HybridDetect 1 strip with astandard Cas reporter. A positive result is shown at top where a Casprotein cleaves the standard reporter, and only one band is seen—due tobinding of the anti-FAM antibody coated nanoparticles to anti-rabbitantibody spotted on the strip. A negative result is shown at bottomwhere the intact reporter binds to a moiety immobilized on the strip,and all of the anti-FAM antibody coated nanoparticles bind at thecontrol line to the FAM molecule on the intact Cas reporter. Results ofrunning samples with target nucleic acids and with a water only controlshowed that even with the water only control, a false positive bandappeared at the test line.

FIG. 73 shows a modified Cas reporter comprising a DNA linker tobiotin-dT (shown as a pink hexagon) bound to a FAM molecule (shown as agreen star). This entire modified Cas reporter was conjugated tomagnetic beads or the surface of the reaction chamber, which wasupstream of the strip. This is shown in the schematic as immobilizationof the modified Cas reporter to the substrate of the DETECTRchamber/bead. During cleavage by a Cas (shown as a yellow pac-man), thebiotin-FAM molecule is released from the DNA linker. Unlike other assayformats, this particular assay format contains the entire Cas cleavagereaction to the reaction chamber. In this assay format, the test-line isthe actual test line and the control line is a true control line. FIG.74 shows the layout of Milenia HybridDetect strips with the modified Casreporter. At top, a positive result is shown, where in the Cas reactionchamber, the Cas protein cleaves the DNA linker segment of the modifiedCas reporter. The biotin-dT/FAM molecule is released and flows down thetest strip binding to streptavidin coated on the test line. An anti-FAMantibody coated gold nanoparticle binds to the biotin-DT/FAM reporter atthe test line. Additionally the anti-FAM antibody coated goldnanoparticle binds to anti-rabbit antibody coated at the flow controlline. At bottom, a negative result is shown where only the anti-FAMantibody coated gold nanoparticle binds to anti-rabbit antibody coatedat the flow control line.

FIG. 75 shows an example of a single target assay format (to left) and amultiplexed assay format (to right). At the top are diagrams showing aschematic of the assay prior to use, anti-FAM antibody coated goldnanoparticles only (on left) or anti-FAM antibody coated goldnanoparticles and anti-ROX antibody coated gold nanoparticles (to right)are upstream of the control and test lines. The control lines arespotted with streptavidin and the test lines are spotted with onlytarget A (left) or target A and target B (right). Assays with positiveresults are shown in the middle schematic and assays with negativeresults are shown in the lowest schematic.

FIG. 76 shows another variation of an assay prior to use (top), an assaywith a positive result (middle left), an assay with a negative result(middle right), and a failed test (bottom). In this assay the flowcontrol is at the left most end of the strip, followed by the test linecoated with anti-IgG rabbit antibody, followed by the control linecoated with streptavidin, followed by gold nanoparticles coated withanti-FAM or anti-biotin antibodies. The Cas reporters are upstream ofthe strip in a reaction chamber. If cleaved the Cas reporter is cleaved(positive result), FAM molecules bind to the anti-FAM coated goldnanoparticles, which subsequently bind at the test line and anti-biotinantibody coated nanoparticles bind at the control line to the DNA/RNAlinker/biotin construct. If the Cas reporter is not cleaved (negativeresult), the intact reporter binds to streptavidin at the control line,where they are subsequently bound by anti-FAM coated gold nanoparticles.

Gold nanoparticle conjugation to anti-biotin antibody. A 100 μl aliquotof anti-biotin antibody was used, with the antibody suspended innuclease free water. 7 μl of the dilute antibody in solution was addedto tubes and reactions were incubated for 30 min in a shaking incubatoryat room temperature. The reaction in each tube was stopped with theaddition of 50 μl of the BSA blocked buffer and the tubes were stored at4C.

Example 37 Conjugation of Oligonucleotides to Peptides/Enzymes forDownstream Use in an Invertase-Coupled Assay for Amperometric Detectionof Target Nucleic Acids Using Programmable Nuclease Systems

This example describes a conjugation method for oligonucleotides topeptides/enzymes for downstream use in an invertase coupled assay foramperometric detection of reactions using a programmable nucleasesystem. Here, DETECTR reactions using CRISPR-Cas systems were used asthe reactions using a programmable nuclease system. The methodsdisclosed herein were developed as alternatives to fluorescence andlateral-flow-immunochromatography readouts of DETECTR reactions andinclude efficient conjugation of an invertase enzyme to a DETECTRreporter using a 3′ thiol modification. The CRISPR-Cas reporter moleculefor use in the invertase-coupled assay for amperometric detection ofDETECTR reactions includes (1) a 5′-Biotin moiety and (2) a 3′-invertaseenzyme. The sequence of the oligowas/5Biosg/TTTTTTTTTTTTTTTTTTTT/3ThioMC3-D/(SEQ ID NO: 169) and theinvertase enzyme was conjugated at the 3′ end. Reagents for theconjugation included invertase from Baker's yeast (S. Cerevisiae, Sigma#I4504), streptavidin magnetic beads (NEB #S1420S),Tris(2-carboxyethyl)phosphine hydrochloride (TCEP, Sigma #C4706),N-Succinimidyl 4-(maleimidomethyl)cyclohexanecarboxylate, SMCC (SMCC,Sigma #M5525), 1M sodium phosphate buffer, pH 7.2 (Tecnova, #P2072),2-(NMorpholino)ethanesulfonic acid (MES, Sigma #76039), sodium chloride5M sterile (VWR #E529), and biotin labelled oligos.

Buffer and solution preparation. Buffers prepared included (1) 0.1MPhosphate Buffer, no NaCl, pH 7.2, (2) 0.1 M Phosphate Buffer, 0.1 MNaCl, pH 7.2, (3) 0.05M MES Buffer, pH 5.5, and (4) 0.05M MES Buffer,with 0.1M NaCl, pH 5.5. TCEP solution, SMCC solution, and invertasesolution was prepared from solids. The DNS reagent was also prepared.

Thiol activation of DNA oligo. The thiol-biotin-labelled oligos (15 μL,1 mM in water) were mixed with TCEP (3 μL, 0.5M in water) in a 1.5-mLmicrocentrifuge tube. The reaction volume was made up to 30 μL with theaddition of 12 μL of eqivalent buffer. The following twelve reactionswere prepared: MB406 with low pH, no salt buffer; MB406 with low pH andsalt buffer; MB406 with PBS, no salt; MB406 with PBS and salt buffer;MB407 with low pH, no salt buffer; MB407 with low pH and salt buffer;MB407 with PBS, no salt; MB407 with PBS and salt buffer; MB408 with lowpH, no salt buffer; MB408 with low pH and salt buffer; MB408 with PBS,no salt; and MB408 with PBS and salt. In each buffer, the volume of DNAoligos was 15 μL, the volume of TCEP was 3 μL, and the volume of bufferwas 12 μL. The reaction was incubated for 3-5 hours in the shakingincubator at 37° C. The reaction was stopped by snap freezing in liquidnitrogen. Microcentrifuge tubes were stored at −20° C. until the nextstep of the reaction. Thiol-activated oligo tubes were removed from thefreezer 3 hours prior to conjugation to activated invertase/or otheractivated proteins/peptides. The tube was first incubated at 37° C. for3 hours and then used in the conjugation reaction

SMCC activation of invertase enzyme. A fresh solution of invertase labstock bottle was prepared. 10 mg of solid was weighed in a clean 1.5 mLmicrocentrifuge tube, 860 μL of buffer A (0.1M NaCl, 0.1 M sodiumphosphate buffer, pH 7.2) was added to make a solution of 20 mg/mL. 1 mgof SMCC was added to a 1.5 mL microcentrifuge tube and the reaction wasinitiated by addition of invertase solution (400 μL, 20 mg/mL in 0.1 MNaCl, 0.1 M sodium phosphate buffer, pH 7.2). The reaction was incubatedin the shaking incubator at 37° C. for 24 hours.

Cleanup of SMCC-activated invertase. The reaction was removed from theshaking incubator (37° C.) after 23 hours and 15 minutes. SMCC-activatedinvertase was washed 8× and resuspended in 400 μL of buffer. Protein wasquantified by the BCA method. Samples were resuspended in either MESbuffer with salt (sample MNT-1), MES buffer without salt (sample MNT-2),or PBS without salt (sample MNT-3).

Re-activation of thiol-DNA oligo. The oligo was removed from −20° C. andincubated in the shaking incubator at 37° C. The reaction was initiatedand incubated in the shaking incubator (37° C.) for 48 hours. Thereaction was removed from the incubator and each reaction contained (1)35 μL of invertase solution, and (2) 30 μL of thiol-DNA oligo solution.

Binding with streptavidin beads. 12.5 μL of streptavidin beads was mixedwith 50 μL of the biotinylated DNA oligo previously conjugated withinvertase enzyme in a 1.5-mL microcentrifuge tube. The reaction wasincubated for 5 minutes at room temperature, beads were washed 5× with50-μL aliquots of Buffer A on a magnetic rack to remove any unbound DNAoligo from the solution, and eluent from all the washes was checked forinvertase activity (and thus inefficient binding between streptavidinand biotin molecules). During the last wash, beads were resuspended with50 μL of Buffer A and beads were stored at 4° C.

Incubation with DNS/Sucrose. A reaction was prepared containing 5 μL of20% sucrose, 30 μL DNS reagent, 25 μL of biotynlated DNA with invertasemoiety. A color change was observed after incubation at high heat (95C).

DNA-Invertase Conjugation. Conjugation was carried out using aheterobifunctional linker sulfo-SMCC. To 30 μl of 1 mM thiol-DNA inMillipore water, 2 μl of 1 M sodium phosphate buffer at pH 5.5 and 2 μlof 30 mM TCEP in Millipore water were added and mixed. This mixture waskept at room temperature for 1 hour and then purified by Amicon-10Kusing Buffer A (0.1 M NaCl, 0.1 M sodium phosphate buffer, pH 7.3, 0.05%TWEEN −20) without TWEEN −20 by 8 times. For invertase conjugation, 400μl of 20 mg/mL invertase in Buffer A without TWEEN −20 was mixed with 1mg of sulfo-SMCC. After vortexing for 5 minutes, the solution was placedon a shaker for 1 hour at room temperature. The mixture was thencentrifuged and the insoluble excess sulfo-SMCC was removed. The clearsolution was then purified by Amicon-100K using Buffer A without TWEEN−20 by 8 times. The purified solution of sulfo-SMCC-activated invertasewas mixed with the above solution of thiol-DNA. The resulting solutionwas kept at room temperature for 48 hours. To remove un-reactedthiol-DNA, the solution was purified by Amicon-100K 8 times using BufferA without TWEEN −20. Conjugation was also carried out usinghomobifunctional linker PDITC. To 60 μl of 1 mM amine-DNA in Milliporewater, 30 μl of Buffer B (0.1 M sodium borate buffer, pH 9.2) were addedand mixed. This solution was further mixed with 20 mg of PDITC dissolvedin 1 mL DMF. The resulting solution was placed on a shaker and kept atroom temperature in the dark for 2 hours. After that, the solution wasmixed with 6 mL of Millipore water and 6 mL 1-butanol. Aftercentrifuging for 15 min, the upper organic phase was discarded. Theaqueous phase was then extracted with 4 mL 1-butanol three times, andpurified by Amicon-10K using Buffer A without TWEEN −20 for 8 times toproduce a PDITC-activated amine-DNA solution. The PDITC activation ratiowas over 90% according to a MALTI-TOF mass spectrum obtained afterdesalting the DNA product. Then, 10 mg of invertase were added to theactivated DNA solution in Buffer A without TWEEN −20 to reach a finalconcentration about 5 mg/mL. The resulting solution was kept at roomtemperature for 48 hours. To remove un-reacted PDITC-activatedamine-DNA, the solution was purified by Amicon-100K 8 times using BufferA without TWEEN −20. Results of the conjugation showed that (1) TWEENwas not necessary for invertase activity; (2) 1 mg/ml invertase reactionlikely finished after 5 min; (3) 2% sucrose input produces red color atRT after ˜15 min; and (4) DNS was not effective for <0.2% sucrose.

Thiol Reduction of Biotin-SG and Conjugation with Invertase/SMCC. Thereaction was initiated by the addition of invertase solution (20 mg/mLinvertase in 0.1 M NaCl, 0.1 M sodium phosphate, pH 7.2) to SMCC. SMCCactivation was tested my adding 3 mg of sulfo-SMCC to either 1200 μL,600 μL, or 60 μL of invertase solution. The reaction incubated whileshaking at 37° C. for approximately 24 hours. The activation reactionswere cleaned up by washing each reaction four times with 300 μL of MESbuffer with salt in a 100 kDa filter. After the final wash, each samplewas resuspended in 400 μL of buffer. Samples were stored at −20° C.

Conjugation of thiol-DNA oligo with SMCC-activated invertase wasperformed by incubating 35 μL of invertase solution with 30 μL ofthiol-DNA oligo solution and incubating at 37° C. for about 48 hours.

Biotinylated DNA oligo conjugated to invertase was bound to streptavidinbeads combining 12.5 μL of streptavidin beads with 50 μL of theconjugated biotin-DNA oligo. The reaction was incubated for 5 min atroom temperature then washed five times with Buffer A on a magnetic rackto remove any unbound DNA oligo. Eluent from the washes was retained forfurther analysis. After the final wash, beads were resuspended in 50 μLof Buffer A.

Invertase activity of the biotin-DNA invertase conjugates was measuredusing a sucrose DNS reaction. Each tested sample was combined withsucrose and DNS reagent and incubated at 95° C. for 5 min. FIG. 99 showsthe DNS sucrose reaction for different tested conditions. The top rowfrom left to right shows the test conditions: 1 pM oligo, 1 mg/mLinvertase; 1 pM oligo, 10 mg/mL invertase; 1 pM oligo, 20 mg/mLinvertase; 1 pM oligo, 1 mg/mL invertase eluent; 1 pM oligo, 10 mg/mLinvertase eluent; 1 pM oligo, 20 mg/mL invertase eluent. The middle rowfrom left to right shows the test conditions: 10 pM oligo, 1 mg/mLinvertase; 10 pM oligo, 10 mg/mL invertase; 10 pM oligo, 20 mg/mLinvertase; 10 pM oligo, 1 mg/mL invertase eluent; 10 pM oligo, 10 mg/mLinvertase eluent; 10 pM oligo, 20 mg/mL invertase eluent; glucosepositive control. The bottom row from left to right shows the testconditions: 100 pM oligo, 1 mg/mL invertase; 100 pM oligo, 10 mg/mLinvertase; 100 pM oligo, 20 mg/mL invertase; 100 pM oligo, 1 mg/mLinvertase eluent; 100 pM oligo, 10 mg/mL invertase eluent; 100 pM oligo,20 mg/mL invertase eluent; buffer negative control (MES with 0.1 MNaCl). A darker solution indicates more active invertase enzyme.

Example 38 Lateral Flow Cleavage Reporters for Programmable NucleaseDiagnostics

This example describes lateral flow cleavage reporters for programmablenuclease diagnostics. Here, CRISPR diagnostics were used as theprogrammable nuclease diagnostics. One design of the Cas reportersdisclosed herein involved tethering the Cas reporter to the reactionchamber, upstream of the lateral flow test strip.

FIG. 77 shows one design of a tethered lateral flow Cas reporter. To theleft is a DNA or RNA linker connecting a functional handle for chemicalconjugation at the 3′ end (amine, thiol, etc.) and a biotin at the 5′end (shown as a diamond) further connected to a FAM reporter molecule.This entire Cas reporter was conjugated to a magnetic bead andimmobilized to the surface of the reaction chamber. After CRISPR-Cascleavage reactions, the DNA/RNA linker was cleaved and the biotin/FAMreporter moiety is released.

FIG. 78 shows a workflow for CRISPR diagnostics using the tetheredcleavage reporter using magnetic beads. First, CRISPR-Cas protein RNPswere incubated with target nucleic acids and magnetic beads wereconjugated to the reporter. Magnetic beads were captured with a magnet,the supernatant was removed, and the sample was placed on a lateral flowstrip with chase buffer.

FIG. 79A shows a FAM-biotin reporter conjugated to magnetic beads,further incubated in the presence or absence of TURBO DNase (Thermo) for15 minutes at 37C. After the incubation period the magnetic beads werepelleted and the supernatant was transferred to a Milenia HybridDetectlateral flow strip (TwistDx). FIG. 79B shows a DIG-biotin reporter,which was conjugated to magnetic beads and incubated in the presence orabsence of TURBO DNase (Thermo) for 15 minutes at 37C. After theincubation period the magnetic beads were pelleted and the supernatantwas transferred to a PCRD lateral flow strip (Abingdon Health). Thebottom panel shows an example of a lateral flow device for multiplexeddetection of FAM-biotin and DIG-biotin reporters that were conjugated tomagnetic beads. FIG. 79C shows a FAM-biotin and DIG-biotin reportersconjugated to magnetic beads. Reporter conjugates were incubated withCas12M08 for 30 min at 37° C. in the presence or absence of 0.5 nMtarget DNA in two separate DETECTR reactions. After the incubationperiod, the magnetic beads were pelleted, and the supernatant wastransferred to a PCRD lateral flow strip (Abingdon Health). Resultsshowed a detection of a specific signal only when the target DNA wasincluded in the reaction, as seen in for Target #2 (FAM-biotin) in thebottom test strip.

FIG. 80 shows photographs of test strips where a tethered cleavagereporter was released by CRISPR-Cas proteins. FAM-biotin reporterconjugated to magnetic beads was incubated with Cas12M08 for 30 minutesat 37C in the presence or absence of target DNA (˜0.5 nM). Two bufferswere tested: buffer 1=MBuffer3, buffer 2=TURBO DNase buffer. The bufferswithout enzyme or target were also tested. After the incubation periodthe magnetic beads were pelleted and the supernatant transferred to aMilenia HybridDetect lateral flow strip (TwistDx).

Tethered cleavage reporters can also be used to multiplex readouts fromCRISPR diagnostics. FAM-biotin and DIG-biotin reporter conjugated tomagnetic beads was incubated with Cas12M08 for 30 minutes at 37C in thepresence or absence of target DNA (˜0.5 nM) in two separate DETECTRreactions. After the incubation period the magnetic beads were pelletedand the supernatant transferred to a PCRD lateral flow strip (AbingdonHealth).

FIG. 81 shows a schematic for an enzyme-reporter system that is filteredby streptavidin-biotin before reaching the reaction chamber. Thereporter structure is shown at left and includes a DNA/RNA linkerconnecting biotin and an enzyme. In the presence of the target (shown attop), Cas proteins cleave the linker in the Cas reaction chamber,leading to binding of biotin to the streptavidin inside of a capturechamber or on a paper strip, and enzymatic activity exhibited in adetection chamber containing the enzyme's substrate. In the absence ofthe target (shown at bottom), Cas proteins do not cleave the linker inthe Cas reaction chamber, leading to binding of the full reporter insideof the capture chamber, and no enzyme (thus, no enzymatic activity) inthe detection chamber containing the enzyme's substrate.

Example 39 Invertase-Nucleic Acid as a Detector Nucleic Acid

This example shows an invertase-nucleic acid as a detector nucleic fordetection of a target nucleic acid in a programmable nuclease system.

FIG. 82 shows an invertase-nucleic acid used for the detection of atarget nucleic acid. The invertase-nucleic acid, immobilized on amagnetic bead, is added to a sample reaction containing Cas protein,guide RNA, and a target nucleic acid. Target recognition activates theCas protein to cleave the nucleic acid of the invertase-nucleic acid,liberating the invertase enzyme from the immobilized magnetic bead. Thissolution is either be transferred to the “reaction mix”, which containssucrose and the DNS reagent and changes color from yellow to red whenthe invertase converts sucrose to glucose or is can be transferred to ahand-held glucometer device for a digital readout.

FIGS. 83A-83C shows an example color change readout by invertase-nucleicacids in reaction mix. DNS reagent produces a colorimetric change wheninvertase converts sucrose to glucose. Free invertase at 0.4 or 4 uM wasreacted with 0-60 mM sucrose for 5, 10, 15 or 30 min at roomtemperature, and samples were heated at 95 C for 10 sec to enhance thecolor change.

Example 40 Enzyme Substrate-Nucleic Acid as a Detector Nucleic Acid

This example shows an enzyme substrate-nucleic acid as a detectornucleic for detection of a target nucleic acid in a programmablenuclease system.

The enzyme substrate-nucleic acid is connected to one of two electrodes.Upon activation of the programmable nuclease (eg. Cas12, Cas13 or Cas14)the enzyme substrates are cleaved from the electrode, resulting indecreased conductance between the electrodes. This resulting change canbe measured by a device such as a glucometer.

Example 41 Sterically Hindered Enzyme-Nucleic Acid as a Detector NucleicAcid

This example shows a sterically hindered enzyme-nucleic acid as adetector nucleic for detection of a target nucleic acid in aprogrammable nuclease system.

A detector nucleic acid comprises an enzyme linked by a nucleic acid(e.g., a ssDNA, ssRNA or a ssDNA/RNA hybrid) to a surface. This enzymeis inhibited sterically by being tethered to the surface, until cleavageof the nucleic acid is initiated by binding of the programmable nucleasecomplexed to a guide nucleic to a target nucleic acid. Release of theenzyme by the cleavage results in the enzyme regaining is function,which can be detected by conversion of the enzyme's substrate to aproduct that results in color, fluorescece, or electrochemical readout.

Example 42 Assay Layouts and Workflows for Programmable Nuclease Systems

This example describes assay layouts and workflows for programmablenuclease systems. Here, DETECTR reactions were used in the programmablenuclease systems. An assay is provided that comprises separate chambersfor amplification and reverse transcription versus a programmablenuclease-based detection assay. The programmable nuclease is a Cas12,Cas13, or Cas14. The sample is a biofluid collected by a swab andinserted into a swab collection reservoir. A pump drives the fluidics inthe assay moving sample from chamber to chamber. A detectable signal iscolorimetric, fluorescence-based, electrochemical and/or generated usingan enzyme (e.g., invertase).

FIG. 84 shows one layout for a DETECTR assay. In this layout a swabcollection cap seals a swab reservoir chamber. Clockwise to the swabreservoir chamber is a chamber holding the amplification reaction mix.Clockwise to the chamber holding the amplification reaction mix is achamber holding the DETECTR reaction mix. Clockwise to this is thedetection area. Clockwise to the detection area is the pH balance well.A cartridge wells cap is shown and seals all the wells containing thevarious reagent mixtures. The cartridge itself is shown as a squarelayer at the bottom of the schematic. To the right is a diagram of theinstrument pipette pump which drives the fluidics in each chamber/welland is connected to the entire cartridge. Below the cartridge is arotary valve that interfaces with the instrument. FIG. 85 shows oneworkflow of the various reactions in the DETECTR assay of FIG. 84 .First, as shown in the top left diagram, a swab may be inserted into the200 μl swab chamber and mixed. In the middle left diagram, the valve isrotated clockwise to the “swab chamber position” and 1 μL of sample ispicked up. In the lower left diagram, the valve is rotated clockwise tothe “amplification reaction mix” position and the 1 μl of sample isdispensed and mixed. In the top right diagram, 2 μL of sample isaspirated from the “amplification reaction mix”. In the right middlediagram, the valve is rotated clockwise to the “DETECTR” position, thesample is dispensed and mixed, and 20 μl of the sample is aspirated.Finally, in the bottom right diagram, the valve is rotated clockwise tothe detection area position and 20 μl of the sample is dispensed. Whilethe rotary valve is in a closed position, the sample is loaded into theswab lysis chamber and sealed using the cap. The sample is thenincubated and mixed by the instrument with the lysis buffer. Followingsample lysis, the rotary valve turns to align with the sample well andaspirates 2 to 4 μL of sample. The rotary valve then turns to align withthe amplification chamber, where the sample is mixed with theamplification mixture. The sample is then aspirated, and the rotaryvalve rotates to the DETECTR chamber. In the DETECTR chamber, the samplemixes with the DETECTR mix. Actuation of the pipette pump mixes thereaction mixtures. The process may then be repeated from theamplification chamber to a second DETECTR chamber.

FIG. 86 shows a modification of the workflow shown in FIG. 85 that isalso consistent with the methods and systems of the present disclosure.At left is the diagram shown at the top right of FIG. 85 . At right isthe modified diagram in which there is a first amplification chambercounterclockwise to the swab lysis chamber and a second amplificationchamber clockwise to the swab lysis chamber. Additionally, clockwise toamplification chamber #2 are two sets, or “duplex,” DETECTR chamberslabeled “Duplex DETECTR Chambers #2” and “Duplex DETECTR Chambers #1,”respectively. FIG. 87 shows breakdown of the workflow for the modifiedlayout shown in FIG. 86 . Specifically, from the swab lysis chamber,which holds 200 μl of sample, 20 μl of the sample can be moved toamplification chamber #1 and 20 μl of the sample can be moved toamplification chamber #2. After amplification in amplification chamber#1, 20 ul of the sample can be moved to Duplex DETECTR Chambers #1 a and20 μl of the sample can be moved to Duplex DETECTR Chambers #1 b.Additionally, after amplification in amplification chamber #2, 20 μl ofthe sample can be moved to Duplex DETECTR Chambers #2a and 20 μl of thesample can be moved to Duplex DETECTR Chambers #2b.

FIG. 88 shows the modifications to the cartridge illustrated in FIG. 86and FIG. 87 . FIG. 89 shows a top down view of the cartridge of FIG. 88. This layout and workflow has a replicate in comparison to the layoutand workflow of FIGS. 84-85 . FIG. 90 shows a layout for a DETECTRassay. Shown at top is a pneumatic pump, which interfaces with thecartridge. Shown at middle is a top down view of the cartridge showing atop layer with reservoirs. Shown at bottom is a sliding valve containingthe sample and arrows pointing to the lysis chamber at left, followingby amplification chambers to the right, and DETECT chambers further tothe right. FIG. 102 shows a schematic of the sliding valve device. FIG.103 shows a layout and workflow for a sliding valve device. In theinitial closed position (i.), the sample is loaded into the sample welland lysed. The sliding valve is then actuated by the instrument, andsamples are loaded into each of the channels using the pippette pump,which dispenses the appropriate volume into the channel (ii.). Thesample is delivered to the amplification chambers by actuating thesliding valve and mixed with the pipette pump (iii.). Samples from theamplification chamber are aspirated into each channel (iv.) and thendispensed and mixed into each DETECTR chamber (v.) by actuating thesliding valve and pipette pump.

Example 43 Hotspot Lung Cancer Assay

This example describes a hotspot lung cancer assay. The hotspot lungcancer assay is carried out using either a one-pot or two-pot workflow.A sample is taken from a subject. The subject is a human or non-humananimal. The sample is a biofluid, such as a blood sample, a serumsample, a plasma sample, a saliva sample, a urine sample, a sputumsample, a mucosal sample, a peritoneal fluid sample, a tissue sample, anexudate, an effusion, or a cell free DNA sample. The assay comprises aprogrammable nuclease that binds to and is activated by a target nucleicacid. The target nucleic acid comprises a mutation, or “hotspot”, in agene correlated with lung cancer. The target nucleic acid is optionallyamplified and the activated programmable nuclease cleaves a reporterthat generates a detectable signal. Generation of the detectable signalindicates presence of hotspot mutations of nucleic acids in a samplefrom a subject, indicating lung cancer.

Example 44 Programmable Nuclease System Assays versus PCR-BasedDetection

This example describes a comparison of the programmable nuclease systemassays disclosed herein to the gold standard: PCR-based methods ofdetecting a target nucleic acid. Here, a DETECTR reaction was used inthe programmable nuclease system assay. Samples were either used as acrude prep for DETECTR assays (only lysed) or purified (lysed, bound,washed, and eluted) for PCR-based methods of detection. A DETECTR assayusing a programmable nuclease (e.g., a Cas protein) was carried out onthe crude sample. The programmable nuclease was activated by the targetnucleic acid in a sample to which it binds via a reverse complementaryguide RNA. The activated programmable nuclease indiscriminately cleavesa reporter generating a fluorescent detectable signal. StandardPCR-based methods were used to also detect the target nucleic acids inthe sample.

FIG. 91 shows a comparison of the DETECTR assays disclosed herein to thegold standard PCR-based method of detecting a target nucleic acid. Shownat top is a flow chart showing a gradient of sample prep evaluation fromcrude (left) to pure (right). Sample prep steps that take a crude sampleto a pure sample include lysis, binding, washing, and eluting. DETECTRassays disclosed herein may only need the sample prep step of lysis,yielding a crude sample. On the other hand, PCR-based methods canrequire lysis, binding, washing, and elution, yielding a very puresample. The graph at bottom shows that, even with a cruder sample prep,the DETECTR assay disclosed herein can identify target nucleic acidsjust as well as current industry standard PCR-based methods ofdetection.

Example 45 Cas13a Detection of DNA

This example describes Cas13a detection of DNA. Cas13a was used todetect RT-LAMP DNA amplicon from Influenza A RNA. FIG. 92A shows aschematic of the workflow including the steps of providing DNA or RNA,LAMP/RT-LAMP amplification, and Cas13a detection. The RT-LAMP reactionwas performed at 55° C. for 30 minutes with a starting RNA concentrationof 10,000 viral genome copies or 0 viral genome copies, as a control.Two different primer sets showed the same results (FIG. 92B and FIG.92C). After completion of the RT-LAMP reaction, 1 μL of amplicon wasadded to a 20 μL Cas13a detection reaction. On-target and off-targetcrRNAs were used to show specific detection by Cas13a at 37° C. of theRT-LAMP DNA amplicon.

FIG. 92A shows a schematic of the workflow which includes providingDNA/RNA, LAMP/RT-LAMP amplification, and Cas13a detection. FIG. 92Bshows Cas13a specific detection of RT-LAMP DNA amplicon with a firstprimer set as measured by background subtracted fluorescence on they-axis. On-target crRNA results are shown by the darker bars andoff-target crRNA control results are shown in lighter bars. A startingRNA concentration of 10,000 viral genome copies is shown in the left twobars and 0 viral genome copies (negative control) is shown in the righttwo bars. FIG. 92C shows Cas13a specific detection of RT-LAMP DNAamplicon with a second primer set as measured by background subtractedfluorescence on the y-axis. On-target crRNA results are shown by thedarker bars and off-target crRNA control results are shown in lighterbars. A starting RNA concentration of 10,000 viral genome copies isshown in the left two bars and 0 viral genome copies (negative control)is shown in the right two bars.

Cas13a recognized ssDNA and RNA target nucleic acids. FIG. 93A shows aCas13 detection assay using 2.5 nM RNA, single-stranded DNA (ssDNA), ordouble-stranded (dsDNA) as target nucleic acids, where detection wasmeasured by fluorescence for each of the targets tested. The reactionwas performed at 37° C. for 20 minutes with both RNA-FQ(RNA-fluorescence quenched reporter) and DNA-FQ reporter substrates.Results showed that Cas13 initiates trans-cleavage activity for RNA-FQfor both RNA and ssDNA targets. Data was normalized to max fluorescencesignal for each reporter substrate. FIG. 93B shows Cas12 detection assayusing 2.5 nM RNA, ssDNA, and dsDNA as target nucleic acids, wheredetection was measured by fluorescence for each of the targets tested.Reactions were performed at 37° C. for 20 minutes with both RNA-FQ andDNA-FQ reporter substrates. Results supported the previously establishedpreference for Cas12 for either ssDNA or dsDNA targets and specificityfor DNA-FQ. Data was normalized to max fluorescence signal for eachreporter substrate. FIG. 93C shows the performance of Cas13 and Cas12 onRNA, ssDNA, and dsDNA targets at various concentrations, where detectionwas measured by fluorescence for each of the targets tested. Reactionswere performed at 37° C. for 90 minutes with both RNA-FQ and DNA-FQreporter substrates. Data was normalized to max fluorescence signal foreach reporter substrate. Results indicated picomolar sensitivity ofCas13 for ssDNA.

Cas13a transc-cleavage activity was found to be specific for RNA whentargeting ssDNA. FIG. 94 shows an Lbu-Cas13a detection assay using 2.5nM ssDNA target with 170 nM of various reporter substrates, whereindetection was measured by fluorescence for each of the reportersubstrates tested. A single RNA-FQ reporter substrate (rep01—FAM-U5) wastested and 13 DNA-FQ reporter substrates were tested. TABLE 12 belowshows the sequence of each of the reporters tested.

TABLE 12 Reporter Sequences Reporter SEQ ID ID NO: Sequence rep01   1/56-FAM/rUrUrUrUrU/3IABkFQ/ rep08 171 /56-FAM/AAAAA/3IABkFQ/ rep09 172/56-FAM/CCCCC/3IABkFQ/ rep10 173 /56-FAM/GGGGG/3IABkFQ/ rep11 174/56-FAM/TTTTT/3IABkFQ/ rep12 175 /56-FAM/TTATTA/3IABkFQ/ rep13   9/56-FAM/TTATTATT/3IABkFQ/ rep14 176 /56-FAM/ATTATTATTA/3IABkFQ/ rep15 10 /56-FAM/TTTTTT/3IABkFQ/ rep16 177 /56-FAM/TTTTTTT/3IABkFQ/ rep17  12/56-FAM/TTTTTTTTTT/3IABkFQ/ rep18 178 /56-FAM/TTTTTTTTTTT/3IABkFQ/ rep19 13 /56-FAM/TTTTTTTTTTTT/3IABkFQ/ rep30 179/FAM/CCGGCAGCCATAACGCCGTGAATACGTT CTGCCGG/BHQ1/

Results indicated that Cas13 trans-cleavage was RNA specific, even whenactivated by ssDNA.

Multiple Cas13 family members detected ssDNA target nucleic acids. FIG.95 A shows the results of Cas13 detection assays for Lbu-Cas13a andLwa-Cas13a using 10 nM or 0 nM of RNA target, where detection wasmeasured by fluorescence resulting from cleavage of reporters over time.Three RNA target sequences were evaluated with corresponding gRNAs.Results showed similar detection of all three target sequences for bothCas13 family members. FIG. 95B shows the results of Cas13 detectionassays for Lbu-Cas13a and Lwa-Cas13a using 10 nM or 0 nM of ssDNAtarget, where detection was measured by fluorescence resulting fromcleavage of reporters over time. Three DNA target sequences and theircorresponding gRNAs, with the same sequence as the RNA targets, wereevaluated. Results showed Cas13 family preferences in ssDNA targetrecognition, with Lbu-Cas13a exhibiting faster detection for sometargets and Lwa-Cas13a exhibiting faster detection for other targets

Cas13 detection of ssDNA was robust at multiple pH values. FIG. 96 showsLbu-Cas13a detection assay using 1 nM RNA (at left) or ssDNA (at right)target in buffers with various pH values ranging from 6.8 to 8.2.Reactions were performed at 37° C. for 20 minutes with RNA-FQ reportersubstrates. Results indicated enhanced Cas13 RNA detection at bufferswith a higher pH (7.9 to 8.2), whereas Cas13 ssDNA detection wasconsistent across pH conditions (6.8 to 8.2).

Cas13 ssDNA targeting preferences were found to be distinct from RNAtargeting preferences. FIG. 97A shows guide RNAs (gRNAs) tiled along atarget sequence at 1 nucleotide intervals. FIG. 97B shows Cas13M26detection assays using 0.1 nM RNA or 2 nM ssDNA target with gRNAs tiledat 1 nucleotide intervals and an off-target gRNA. Guide RNAs were rankedby their position along the target sequence. FIG. 97C shows data fromFIG. 97B ranked by performance of ssDNA. Results showed that gRNAperformance on ssDNA did not correlate with the performance of the samegRNAs on RNA. FIG. 97D shows performance of gRNAs on RNA split by theidentity of the nucleotide on the target that is 3′ of the targetsequence. Results indicated that there are high performing gRNAs on RNAsregardless of target nucleotide identity at this position. FIG. 97Eshows performance of gRNAs on RNA split by the identity of thenucleotide on the target that is 3′ of the target sequence. Resultsindicated that a G in the target at this position performed worse thanother gRNAs.

Cas13a detected DNA generated by nucleic acid amplification methods(PCR, LAMP). FIG. 98A shows Lbu-Cas13a detection assays using 1 μL ofDNA amplicon from various LAMP isothermal nucleic acid amplificationreactions. LAMP conditions tested included 6-primer with bothloop-forward (LF) and loop-reverse (LB), asymmetric LAMP with LF only,and asymmetric LAMP with LB only. All tested LAMP reactions generated anLbu-Cas13a compatible DNA target. FIG. 98B shows Cas13M26 detectionassays using various amounts of PCR reaction as a DNA target. Resultsindicated that PCR generated enough ssDNA intermediates to enable Cas13detection.

Example 46 Layouts and Workflows for Programmable Nuclease Systems

This example describes assay layouts and workflows for programmablenuclease systems. Here, DETECTR reactions are used in the programmablenuclease system. An assay is provided that comprises separate chambersfor amplification and reverse transcription versus a programmablenuclease-based detection assay. The programmable nuclease is a Cas12,Cas13, or Cas14. The sample is a biofluid collected by a swab andinserted into a swab collection reservoir. A pump drives the fluidics inthe assay moving sample from chamber to chamber. A detectable signal iscolorimetric, fluorescence-based, electrochemical and/or generated usingan enzyme (e.g., invertase).

FIG. 100A shows a schematic of a pneumatic valve device. A pipette pumpaspirates and dispenses samples. An air manifold is connected to apneumatic pump to open and close the normally closed valve. Thepneumatic device moves fluid from one position to the next and isolatesunused parts of the system. The pneumatic design has reduced channelcross talk compared to other devices. FIG. 100B shows a schematic of acartridge for use in the pneumatic valve device. The normally closedvalves (one such valve is indicated by an arrow) comprise an elastomericseal on top of the channel to isolate each chamber from the rest of thesystem when the chamber is not in use. The pneumatic pump uses air toopen and close the valve as needed to move fluid to the necessarychambers within the cartridge. The cartridge is able to incorporatemultiple different sample media. The cartridge can accommodate lysisbuffer volumes of 200 μL and perform incubation steps, for example, a 10minute incubation. The cartridge accommodates aspiration of two 2 μLsamples from up to four amplification chambers. The two samples can bedispensed into the corresponding detection chambers with limited crosscontamination between amplification chambers or detection chambers. Thecartridge accommodates transfer of 1-2 μL of lysed sample from thesample input chamber to an amplification chamber. The cartridge maycomprise up to four amplification chambers, with two detection chambersper amplification chamber, for a total of up to eight detectionchambers. Each DETECTR chamber may be imaged, for example by aspectrometer. As shown in FIG. 100 and illustrated in FIG. 101 , thecartridge may have two amplification chambers and two detection chambersper amplification chamber.

FIG. 101 shows a valve circuitry layout for the pneumatic valve DETECTRdevice. The biofluid sample is placed in the sample well while allvalves are closed, as shown at (i.). The sample is lysed in the samplewell. The lysed sample is moved from the sample chamber to a secondchamber by opening the first quake valve, as shown at (ii.), andaspirating the sample using the pipette pump. The sample is then movedto the first amplification chamber by closing the first quake valve andopening a second quake valve, as shown at (iii.) where it is mixed withthe amplification mixture. After the sample is mixed with theamplification mixture, it is moved to a subsequent chamber by closingthe second quake valve and opening a third quake valve, as shown at(iv). The sample is moved to the detection chamber by closing the quickthird valve and opening a quick fourth valve, as shown at (v). Thedetection chamber comprises the programmable nuclease. If a targetnucleic acid is present in the sample, a detectable signal may beproduced. The detectable signal may be imaged in the detection chamber.The sample can be moved through a different series of chambers byopening and closing a different series of quake valves, as shown at(vi). Actuation of individual valves in the desired chamber seriesprevents cross contamination between channels.

FIG. 106 shows a schematic of the top layer of a cartridge of apneumatic valve device of the present disclosure, highlighting suitabledimensions. The schematic shows one cartridge that is 2 inches by 1.5inches. FIG. 107 shows a schematic of a modified top layer of acartridge of a pneumatic valve device of the present disclosure adaptedfor electrochemical dimension. In this schematic, three lines are shownin the detection chambers (4 chambers at the very right). These threelines represent wiring (or “metal leads”), which is co-molded,3D-printed, or manually assembled in the disposable cartridge to form athree-electrode system. Electrodes are termed as working, counter, andreference. Electrodes can also be screenprinted on the cartridges.Metals used can be carbon, gold, platinum, or silver.

Example 47 dsDNA Enrichment for Type V Programmable Nuclease SNP DETECTRReactions

This example describes dsDNA enrichment for type V programmable nucleaseSNP DETECTR reactions. Type V programmable nucleases, for example Cas12,typically have high specificity for detection of SNPs in dsDNAsubstrates. Amplification, for example using PCR, allele-specific PCR,or isothermal amplification, can generate both ssDNA and dsDNAsubstrates, which may reduce the degree of specificity achieved by theCas12 programmable nuclease for SNPs. Removal of ssDNA productsexchanges specificity for SNP detection by type V programmablenucleases, for example Cas12 programmable nucleases.

FIG. 104 illustrates a method to enrich for dsDNA products followingamplification. The method involves treating the reaction with a ssDNasewith 3′ to 5′ exonuclease activity that is inhibited by phosphorothiate.The ssDNas may be an Exonuclease I, including both wild type E. coli andthermolabile exonucleases; Exonulcease III, including E. coliexonucleases; Exonuclease T; and RecJf. A target nucleic acid isamplified using PCR, allele-specific PCR, or isothermal amplification.The amplification process results in a mixture of dsDNA and ssDNAproducts. A ssDNase 3′ to 5′ exonuclease I, exonuclease III, exonulceaseT, or RecJf is added to the amplified target nucleic acid sample. ThessDNase degrades ssDNA, leaving only dsDNA products. The presence of aSNP of interest in the target dsDNA is then detected using a type V SNPDETECTR reaction. To enable one-pot reactions, fully phosphorothioatedprimers and reporters may be incorporated.

Example 48 Determination of the Maximum Volume of LAMP Amplicon in aCas12M08 DETECTR Reaction Before Assay Inhibition

This example describes the determination of the maximum volume of LAMPamplicon that may be used in a Cas12M08 DETECTR reaction before theassay is inhibited. A concentrated complexing reaction (40 nM R778crRNA, 40 nM Cas12M08 in MBuffer 3) was prepared at incubated at 37° C.for 30 minutes. The concentrated complexing reaction (2.5 μL) wascombined with rep33 reporter substrate (0.02 μL of 100 nM reportersubstrate).

LAMP amplicon product solutions were prepared by combining differentvolumes of LAMP product with buffer (MBuffer3) to a total volume of 17.5μL. Buffer was combined with 0 μL, 2 μL, 4 μL, 6 μL, 8 μL, 10 μL, 12 μL,or 14 μL of LAMP product. Buffer solutions containing different volumesof LAMP amplicon product were added to individual wells (17.5 μL) of anassay plate. Concentrated Cas12a complexing reaction with reportersubstrate (2.5 μL) was added to each well containing the 17.5 μL of LAMPamplicon product. The assay plate was sealed, and the plate was shakento mix. The fluorescence of each well was then read on a plate reader.

FIG. 105 shows the raw fluorescence produced in each well containing aCas12a complexing reaction with different volumes of LAMP ampliconproduct. A higher fluorescence value is indicative of better assayperformance. Addition of 2 μL of LAMP amplicon per DETECTR reactionshowed the best assay performance (highest fluorescence) of any of theconditions tested. Increasing volumes of LAMP amplicon resulted in adecreasing assay performance, as measured by fluorescence.

While preferred embodiments of the present disclosure have been shownand described herein, it will be obvious to those skilled in the artthat such embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the disclosure. It should beunderstood that various alternatives to the embodiments of thedisclosure described herein may be employed in practicing thedisclosure. It is intended that the following claims define the scope ofthe disclosure and that methods and structures within the scope of theseclaims and their equivalents be covered thereby.

What is claimed is:
 1. A method of assaying for a presence of a target nucleic acid in a sample comprising a plurality of nucleic acids, the method comprising the steps of: a) contacting the sample comprising the plurality of nucleic acids to: i) a guide nucleic acid comprising RNA having at least 10 nucleotides reverse complementary to a sequence in the target nucleic acid in the plurality of nucleic acids; ii) a programmable nuclease, wherein the programmable nuclease is activated upon binding of the guide nucleic acid to the target nucleic acid, or an amplicon thereof; iii) a reporter comprising a detector nucleic acid and a detection moiety, wherein the detector nucleic acid of the reporter comprises a nucleotide sequence which is capable of being trans cleaved by the programmable nuclease upon activation; and iv) reagents for amplification, b) amplifying the target nucleic acid if present in the plurality of nucleic acids, c) assaying for a first signal produced by trans cleavage of the detector nucleic acid of the reporter by the programmable nuclease, wherein trans cleavage by the programmable nuclease is activated upon hybridization of the guide nucleic acid to the target nucleic acid or an amplicon thereof, and d) comparing the first signal to a second signal generated from a positive control, a negative control, or a combination thereof, thereby determining the presence of the target nucleic acid in the sample, wherein the amplifying of step b) and the assaying of step c) are performed in a single reaction volume.
 2. The method of claim 1, wherein, when the target nucleic acid is RNA, the method further comprises reverse transcribing the target nucleic acid to produce a cDNA and amplifying the cDNA to produce the amplicon.
 3. The method of claim 2, wherein the reverse transcribing and the amplifying of the cDNA are performed in the single reaction volume.
 4. The method of claim 1, wherein the reagents for amplification comprise a forward primer, a reverse primer, a dNTP, and a polymerase.
 5. The method of claim 1, wherein the forward primer, the reverse primer, or both comprises a T7 promoter.
 6. The method of claim 1, wherein the amplifying of step b) comprises thermal amplification.
 7. The method of claim 1, wherein the amplifying of step b) comprises isothermal amplification.
 8. The method of claim 1, wherein the amplifying of step b) comprises recombinase polymerase amplification (RPA), transcription mediated amplification (TMA), strand displacement amplification (SDA), helicase dependent amplification (HDA), loop mediated amplification (LAMP), rolling circle amplification (RCA), single primer isothermal amplification (SPIA), ligase chain reaction (LCR), simple method amplifying RNA targets (SMART), improved multiple displacement amplification (IMDA), or nucleic acid sequence-based amplification (NASBA).
 9. The method of claim 1, wherein the amplifying of step b) comprises recombinase polymerase amplification (RPA).
 10. The method of claim 1, wherein the amplifying of step b) comprises loop mediated amplification (LAMP).
 11. The method of claim 1, wherein the sample comprises a cell and wherein the method is performed in a device comprising: a) a first chamber comprising the sample and a buffer for lysing the cell; and b) a second chamber, fluidically connected to the first chamber, wherein the second chamber comprises the programmable nuclease and the reporter; and wherein the amplifying of claim 1, step b) is performed in the second chamber.
 12. The method of claim 11, wherein the second chamber is coupled to a measurement device for measuring the first signal produced by cleavage of the detector nucleic acid of the reporter.
 13. The method of claim 1, wherein the method is performed in a device comprising: a) a sliding layer comprising a channel with an opening at a first end of the channel and an opening at a second end of the channel; and b) a fixed layer comprising: i) a first chamber having an opening, wherein the first chamber comprises the sample; ii) a second chamber having an opening, wherein the second chamber comprises the programmable nuclease and the reporter; iii) a first side channel having an opening aligned with the opening of the first chamber; and iv) a second side channel having an opening aligned with the opening of the second chamber, wherein the sliding layer and the fixed layer move relative to each other to fluidically connect the first chamber and the first side channel via the opening at the first end of the channel, the opening at the second end of the channel, the opening of the first chamber, and the opening of the first side channel, wherein the sliding layer and the fixed layer move relative to each other to fluidically connect the second chamber and the second side channel via the opening at the first end of the channel, the opening at the second end of the channel, the opening of the second chamber, and the opening of the second side channel, and wherein the amplifying of claim 1, step b) is performed in the second chamber.
 14. The method of claim 13, wherein the second chamber is coupled to a measurement device for measuring the first signal produced by cleavage of the detector nucleic acid of the reporter.
 15. The method of claim 1, wherein the method is performed in a device comprising: a) a chamber comprising the programmable nuclease and the reporter, wherein the reporter further comprises an affinity molecule; and b) a lateral flow strip comprising: i) a first region comprising a capture molecule specific for the affinity molecule; and ii) a second region comprising an antibody, wherein the first region is upstream of the second region and the chamber is upstream of the lateral flow strip and wherein the affinity molecule binds to the capture molecule, and and wherein the amplifying of claim 1, step b) is performed in the chamber.
 16. The method of claim 15, wherein the affinity molecule is conjugated to a 3′ end or a 5′ end of the detector nucleic acid of the reporter, and wherein the affinity molecule is directly conjugated to the detection moiety.
 17. The method of claim 1, wherein the programmable nuclease is a Type VI CRISPR/Cas enzyme.
 18. The method of claim 17, wherein the Type VI CRISPR/Cas enzyme is a programmable Cas13 nuclease.
 19. The method of claim 1, wherein the programmable nuclease is a Type V CRISPR/Cas enzyme.
 20. The method of claim 19, wherein the Type V CRISPR/Cas enzyme is a programmable Cas12 nuclease.
 21. The method of claim 1, wherein the programmable nuclease comprises a RuvC nuclease domain.
 22. The method of claim 1, wherein the programmable nuclease comprises a HEPN nuclease domain.
 23. The method of claim 1, wherein the programmable nuclease is an RNA-guided nuclease.
 24. The method of claim 1, wherein the reagents for amplification are added sequentially to the single reaction volume.
 25. The method of claim 1, wherein the reporter is: a ssDNA molecule or a hybrid reporter molecule comprising at least one ribonucleotide and at least one deoxyribonucleotide.
 26. The method of claim 1, wherein the reporter or the guide nucleic acid is immobilized to a surface.
 27. The method of claim 26, wherein the surface is a surface of a chamber or a surface of a bead.
 28. The method of claim 1, wherein the detection moiety comprises a fluorophore which is attached to a quencher by the detector nucleic acid, and wherein, upon the trans cleavage of the detector nucleic acid, the fluorophore generates the first signal, wherein the first signal is detected as a positive signal, indicating the presence of the target nucleic acid.
 29. The method of claim 1, further comprising comparing the first signal to a third signal, wherein the third signal is present prior to the cleavage of the detector nucleic acid of the reporter and the first signal is produced upon the cleavage of the detector nucleic acid of the reporter, thereby determining the presence of the target nucleic acid.
 30. The method of claim 1, wherein the first signal is absent prior to the cleavage of the detector nucleic acid of the reporter and is produced upon the cleavage of the detector nucleic acid of the reporter, thereby determining the presence of the target nucleic acid.
 31. The method of claim 1, wherein the reporter is suspended in solution.
 32. The method of claim 1, wherein the first signal is a calorimetric signal, a potentiometric signal, an amperometric signal, an optical signal, or a piezo-electric signal.
 33. The method of claim 1, wherein, when the target nucleic acid is DNA, the method further comprises in vitro transcribing the target nucleic acid to produce an RNA and amplifying the RNA to produce the amplicon, wherein amplifying the RNA comprises reverse transcribing the RNA to produce a cDNA and amplifying the cDNA to produce the amplicon.
 34. The method of claim 33, wherein the in vitro transcribing and the amplifying of the RNA is performed in the single reaction volume. 